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Yoon, E.

Publications and source records attributed to Yoon, E..

At least 19 recordsLinked to original sources
bioRxiv2026

Sharp wave-ripple clusters enhance hippocampal-neocortical engagement for memory consolidation

Hippocampal sharp wave-ripples (SPW-Rs), neocortical slow oscillations, and thalamocortical sleep spindles are hypothesized to provide a temporal framework for coordinated information transfer during memory consolidation. Hippocampal replay supports this process, yet replayed sequences often unfold across multiple SPW-Rs, suggesting that individual ripples may not constitute the fundamental unit of hippocampal output. Here, using large-scale electrophysiological recordings from the hippocampus and retrosplenial cortex, we show that hippocampal output is organized into clusters of SPW-Rs (cSPW-Rs) during UP states, which are often phase-locked to spindle troughs. Extending this approach with wide-field imaging and unsupervised latent-variable modeling, we found that cSPW-Rs enhanced segregation between the default mode and somatomotor networks and preferentially replayed spatially extended maze trajectories following learning. We propose that SPW-R clusters enable reverberating hippocampal-cortical spike exchange and the concatenation of sequential experiences, establishing ripple clusters as a previously unrecognized syntactic unit of hippocampal-neocortical dialogue.

neuroscience↗
bioRxiv2025

cPLA2α Targeting to Exosomes Connects Nuclear Deformation to LTB4-Signaling During Neutrophil Chemotaxis

Efficient neutrophil chemotaxis requires the integration of mechanical forces and lipid-mediated signaling. While the signaling lipid leukotriene B4 (LTB4) reinforces cellular polarity, how mechanical cues regulate its production remains unclear. We now show that cytosolic phospholipase A2 (cPLA2), which is essential for the synthesis of LTB4, functions as a nuclear curvosensor. cPLA2 responds to nuclear constrictions by localizing to ceramide-rich inner nuclear membrane microdomains and incorporating onto the exofacial surface of nuclear envelope-derived exosomes. This unique topology enables localized LTB4 synthesis, which promotes myosin light chain II phosphorylation, and sustains polarity and directional persistence after constriction. In neutrophils squeezing through small constrictions, loss of cPLA2 impairs nuclear curvature sensing, exosomal LTB4 production, and post-constriction motility. These findings uncover a cPLA2-dependent mechano-chemical axis linking nuclear architecture to chemotactic efficiency and offering new strategies to modulate inflammatory responses.

cell biology↗
bioRxiv2025

Analysis of 14q12 microdeletions reveals novel regulatory loci for the neurodevelopmental disorder-related gene, FOXG1

Up to 17% of neurodevelopmental disorders (NDDs) can be explained by pathogenic structural variants (SVs) that disrupt coding regions and elicit gene dosage defects. However, noncoding SVs which can perturb cis-regulatory elements (CREs) and downstream gene expression are understudied. In this study, we describe multiple 14q12 deletions downstream of NDD-related gene FOXG1 in individuals with overlapping phenotypes of FOXG1 haploinsufficiency. We show that deletion of a minimum region of overlap (MRO) reduced FOXG1 expression, disrupted CREs and altered FOXG1s native genomic interactions. Deleting the MRO did not fully eliminate FOXG1 expression, indicating that multiple CREs likely cooperate to regulate FOXG1 and would need to be deleted to completely prevent expression. The transcriptomic profiles of MRO loss overlap in part with FOXG1 loss, including direct FOXG1 targets, indicating converging molecular pathways. These findings expand the scope of FOXG1s complex regulatory region, and more broadly, of regulatory SVs in NDD susceptibility.

genetics↗
bioRxiv2024

Optogenetic stimulation of a cortical biohybrid implant guides goal directed behavior

Brain-computer interfaces (BCIs) hold exciting therapeutic potential, but tissue damage caused by probe insertion limits channel count. Biohybrid devices, in which the cell-device interface is crafted in the laboratory, hold promise to address this limitation, but these devices have lacked a demonstration of their applicability for BCI. We developed a biohybrid approach to engraft optogenetically-enabled neurons on the cortical surface housed in a 2D-scaffold of circular microwells. The engrafted neurons survived, exhibited spontaneous activity, and integrated with the host brain several weeks after implantation. We then trained mice with biohybrid implants to perform an optical stimulation task and showed that they could effectively report optogenetic stimulation of their neural graft. This demonstration shows that a cortical biohybrid implant can be used to transmit information to the brain of an implanted animal.

neuroscience↗
bioRxiv2024

Identification of the MRTFA/SRF pathway as a critical regulator of quiescence in cancer.

Chemoresistance is a major driver of cancer deaths. One understudied mechanism of chemoresistance is quiescence. We used single cell culture to identify, retrieve, and RNA-Seq profile primary quiescent ovarian cancer cells (qOvCa). We found that many qOvCa differentially expressed genes are transcriptional targets of the Myocardin Related Transcription Factor/Serum Response Factor (MRTF/SRF) pathway. We also found that genetic disruption of MRTF-SRF interaction, or an MRTF/SRF inhibitor (CCG257081) impact qOvCa gene expression and induce a quiescent state in cancer cells. Suggesting a broad role for this pathway in quiescence, CCG257081 treatment induced quiescence in breast, lung, colon, pancreatic and ovarian cancer cells. Furthermore, CCG081 (i) maintained a quiescent state in patient derived breast cancer organoids and, (ii) induced tumor growth arrest in ovarian cancer xenografts. Together, these data suggest that MRTF/SRF pathway is a critical regulator of quiescence in cancer and a possible therapeutic target. SignificanceQuiescence is a critical driver of chemoresistance. The MRFT-SRF pathway regulates cancer cell quiescence and inhibiting the MRTF-SRF pathway can prevent the outgrowth of quiescent cancer cells and improve cancer outcomes.

cancer biology↗
bioRxiv2024

Dual-color micro-LEDs integrated neural interface for multi-control optogenetic electrophysiology

Over recent decades, optogenetics has become a pivotal technique for elucidating the functionality of neuronal circuits in living organisms. By genetically modifying specific cells within targeted tissues to respond to particular optical stimuli, researchers can achieve precise activation or inhibition of these cells. This capability enables detailed investigations of neural circuitry with unprecedented accuracy. However, there is a rising need for hardware that supports bidirectional control in conjunction with electrophysiological recording. A significant challenge in this domain is the compact integration of dual light sources and a recording system. This study addresses this challenge through the development of a novel microfabrication and assembly technique for embedding dual-color micro-LEDs and recording electrodes into a Michigan-type neural probe structure, designated as DuoLite (Dual-color micro-LEDs Integrated Neural-Interface Optoelectrode for Multi-Control Optogenetic Electrophysiology). We present two device variants: (a) a small-group and (b) a large-group cell-targeted design, each incorporating micro-LEDs with a minimal area of <100 m2 for both red and blue light. The design and assembly techniques for integrating all three components within a shank width of <100 m are thoroughly detailed, and the functionality of the devices is validated through in vivo experiments.

bioengineering↗
bioRxiv2024

Acoustic target strengths and swimbladder morphology of Chub mackerel Scomber japonicus in the Northwest Pacific Ocean

The Northwest Pacific chub mackerel (Scomber japonicus) is one of the most productive, economically important fishery resources worldwide. Due to fluctuations in their abundance and distribution, there is a pressing need to accurately assess this species and to ensure total allowable catch limits are followed. Acoustic target strength (TS; dB) measurements of Scomber japonicus were conducted at 38, 70, and 120 kHz using a split-beam echosounder of individuals from nine size groups (mean fork length, 10.8[~]28.3 cm) swimming freely in a net cage within a seawater tank. An underwater camera was utilized to simultaneously measure the swimming angle. A least-squares regression analysis revealed that when the slope was constrained to 20, as per the generally applicable morphometric equation, the resulting values for the constant term (b20) were -67.7, -66.6, and - 67.3 dB at 38, 70, and 120 kHz, respectively. The mean swimming angle of S. japonicus across the groups was -10.5[~]9.6{degrees} (standard deviation (SD), 16.3[~]33.3{degrees}). In addition, the ratio of swimbladder height to swimbladder length, swimbladder length to fork length, and tilt angle of the swimbladder (mean {+/-} SD) were 0.191 {+/-} 0.060, 0.245 {+/-} 0.055, and 9.6 {+/-} 3.0{degrees}, respectively. These results can be used for the acoustic stock assessment of S. japonicus in the Northwest Pacific Ocean.

animal behavior and cognition↗
bioRxiv2024

Self-Assembled Origami Neural Probes for Scalable, Multifunctional, Three-Dimensional Neural Interface

Flexible intracortical neural probes have drawn attention for their enhanced longevity in high-resolution neural recordings due to reduced tissue reaction. However, the conventional monolithic fabrication approach has met significant challenges in: (i) scaling the number of recording sites for electrophysiology; (ii) integrating of other physiological sensing and modulation; and (iii) configuring into three-dimensional (3D) shapes for multi-sided electrode arrays. We report an innovative self-assembly technology that allows for implementing flexible origami neural probes as an effective alternative to overcome these challenges. By using magnetic-field-assisted hybrid self-assembly, multiple probes with various modalities can be stacked on top of each other with precise alignment. Using this approach, we demonstrated a multifunctional device with scalable high-density recording sites, dopamine sensors and a temperature sensor integrated on a single flexible probe. Simultaneous large-scale, high-spatial-resolution electrophysiology was demonstrated along with local temperature sensing and dopamine concentration monitoring. A high-density 3D origami probe was assembled by wrapping planar probes around a thin fiber in a diameter of 80[~]105 m using optimal foldable design and capillary force. Directional optogenetic modulation could be achieved with illumination from the neuron-sized micro-LEDs (LEDs) integrated on the surface of 3D origami probes. We could identify angular heterogeneous single-unit signals and neural connectivity 360{degrees} surrounding the probe. The probe longevity was validated by chronic recordings of 64-channel stacked probes in behaving mice for up to 140 days. With the modular, customizable assembly technologies presented, we demonstrated a novel and highly flexible solution to accommodate multifunctional integration, channel scaling, and 3D array configuration.

neuroscience↗
bioRxiv2023

A compact, ultrahigh-density headstage with high-fidelity hybrid integration for large-scale deep-brain opto-electrophysiology

Recent neuroscientific research seeks to comprehend the sophisticated deep-brain networks of neural circuits consisting of large scale neuronal ensembles across multiple brain regions. An ideal way to unveil the complex connectome might be stimulating individual neurons with high spatial resolution in a broad range of brain, while seamlessly monitoring the correspondent neuronal activities. Optogenetics is known as a key technology to enable such a goal thanks to its high spatial and temporal selectivity in neuromodulation. Existing silicon probe technologies have been able to partially achieve such a goal by recording broad region of brain activities through multiple electrodes per shank, but those cannot complete perfect coverage due to the limited channel counts for the optogenetic stimulation. Here, we present an high-channel-count optogenetic system with simultaneous 256 recoding and 128 optogenetic stimulation sites, exhibiting the highest channel density ever reported, enabled by a flexible polyimide cable-based hybrid-integration of a low-stimulation-artifact micro-LED ({micro}LED) opto-electrode with a low-power and -noise, area-efficient CMOS interfacing integrated-circuit (IC). The presented optogenetic system provides 256-neuron-size electrodes (11 x 15 {micro}m2) with a 40 {micro}m inter-electrode pitch for high spatial oversampling in recording and 128-soma-size {micro}LEDs (8 x 11 {micro}m2) with a 20 {micro}m inter-LED pitch for single-cell resolution in stimulation, resulting in a vertical span of 640 {micro}m and a horizontal span of 2,100 {micro}m with a total 8 shanks. For versatility in optogenetics-based experiments from small rodents to primates with user-preferable settings, the system base that provides programmability of recording and stimulation parameters and rest of signal processing, such as filtering, digitization, and data transmission including serial peripheral interface (SPI) has also been designed within small area of 23.8 x 28.8 mm2 with only 3.5-gram weight, resulting in the highest channel density both in size (0.56 channels/mm2) and weight (109.71 channels/gram) among the state-of-the-art optogenetics-based neuromodulation systems. To verify the system operation in vivo, a compact optogenetics headstage has been also fabricated. Using the prepared optogenetic headstage, 169 isolated neurons have been observed with various stimulation intensities. The results offered in this article indicate that the presented hybrid integrated ultrahigh-density, high-channel-count headstage can be used to realize the massive-scale in-depth brain studies with optogenetics.

bioengineering↗
bioRxiv2023

Simultaneous Electrophysiology and Optogenetic Perturbation of the Same Neurons in Chronically Implanted Animals using microLED Silicon Probes

Optogenetics are a powerful tool for testing how a neural circuit influences neural activity, cognition, and behavior. Accordingly, the number of studies employing optogenetic perturbation has grown exponentially over the last decade. However, recent studies have highlighted that the impact of optogenetic stimulation/silencing can vary depending on the construct used, the local microcircuit connectivity, extent/power of illumination, and neuron types perturbed. Despite these caveats, the majority of studies employ optogenetics without simultaneously recording neural activity in the circuit that is being perturbed. This dearth of simultaneously recorded neural data is due in part to technical difficulties in combining optogenetics and extracellular electrophysiology. The recent introduction of LED silicon probes, which feature independently controllable miniature LEDs embedded at several levels of each of multiple shanks of silicon probes, provides a tractable method for temporally and spatially precise interrogation of neural circuits. Here, we provide a protocol addressing how to perform chronic recordings using LED probes. This protocol provides a schematic for performing causal and reproducible interrogations of neural circuits and addresses all phases of the recording process: introduction of optogenetic construct, implantation of the LED probe, performing simultaneous optogenetics and electrophysiology in vivo, and post-processing of recorded data. SUMMARYThis method allows a researcher to simultaneously perturb neural activity and record electrophysiological signal from the same neurons with high spatial specificity using silicon probes with integrated LEDs. We outline a procedure detailing all stages of the process for performing reliable LED experiments in chronically implanted rodents.

neuroscience↗
bioRxiv2023

Caf1 regulates Ash1 histone methyltransferase activity via sensing unmodified histone H3.

Histone modifications are one of key mechanisms to regulate gene expression. Ash1 is a histone H3K36 methyltransferase and involved in gene activation. Ash1 forms a large complex with Mrg15 and Caf1/p55/Nurf55/RbAp48 (AMC complex). Ash1 subunit alone has very low activity due to the auto-inhibition and the binding of Mrg15 releases the auto-inhibition. Caf1 is a scaffolding protein commonly found in several chromatin modifying complexes. Caf1 has an ability to sense unmodified histone H3K4 residue. However, the role of Caf1 in AMC complex has not been investigated. Here, we dissected the interaction among the AMC complex subunits, revealing that Caf1 uses the histone H4 binding pocket to interact with Ash1 near the histone binding module cluster. Furthermore, we show that H3K4 methylation inhibits AMC HMTase activity via Caf1 sensing unmodified histone H3K4 to regulate the activity in an inter-nucleosomal manner, suggesting that there is a crosstalk between H3K4 and H3K36 methylations. Our work reveals a delicate regulatory mechanism of AMC histone H3K36 methyltransferase complex.

biochemistry↗
bioRxiv2022

flexLiTE: flexible micro-LED integrated optoelectrodesfor minimally-invasive chronic deep-brain study

Understanding complex neuronal circuitry and its functions of a living organism requires a specialized tool which is capable of recording a large ensemble of neuronal signals at single cell resolution and modulating neuronal activities selectively in the target region of brains with high spatiotemporal resolution, while sustaining long-term chronic operation without significant tissue degeneration or device shifts. We hereby present an ultra-flexible, minimally-invasive, Michigan-type neural probe for chronic opto-electrophysiology studies: flexLiTE (flexible micro-LED integrated optoelectrodes). flexLiTE incorporates monolithically integrated, soma-sized inorganic micro-LEDs (12 individually operated) and 32 recording electrodes. Both stimulation and recording modalities were achieved by stacking two modules on a flexible substrate: one with micro-LEDs for neuromodulation and the other with recording sites, resulting in a 115 m-wide,12 m-thick, 10 mm-long optoelectrode. From prototype devices, we demonstrated the reliable operation of flexLiTEs for recording and modulation of hippocampal neurons in a freely moving mice for over [~]8 month.

bioengineering↗
bioRxiv2022

Ultra-flexible and Stretchable Intrafascicular Peripheral Nerve Recording Device with Axon-dimension, Cuff-less Microneedle Electrode Array

Peripheral nerve mapping tools with higher spatial resolution are needed to advance systems neuroscience, and potentially provide a closed-loop biomarker in neuromodulation applications. Two critical challenges of microscale neural interfaces are (i) how to apply them to small peripheral nerves, and (ii) how to minimize chronic reactivity. We developed a flexible microneedle nerve array (MINA), which is the first high-density penetrating electrode array made with axon-sized silicon microneedles embedded in low-modulus thin silicone. We present the design, fabrication, acute recording, and chronic reactivity to an implanted MINA. Distinctive units were identified in the rat peroneal nerve. We also demonstrate a long-term, cuff-free, and suture-free fixation manner using rose bengal as a light-activated adhesive for two timepoints. The tissue response at 1-week included a sham (N=5) and MINA-implanted (N=5) group, and the response at 6-week also included a sham (N=3) and MINA-implanted (N=4) group. These conditions were quantified in the left vagus nerve of rats using histomorphometry. Micro-CT was added to visualize and quantify tissue encapsulation around the implant. MINA demonstrated a reduction in encapsulation thickness over previously quantified interfascicular methods. Future challenges include techniques for precise insertion of the microneedle electrodes and demonstrating long-term recording.

neuroscience↗
bioRxiv2022

Cryo-EM structure of human somatostatin receptor 2 complex with its agonist somatostatin delineates the ligand binding specificity

Somatostatin is a peptide hormone regulating endocrine systems through binding to G-protein-coupled somatostatin receptors. somatostatin receptor 2 (SSTR2) is one of the human somatostatin receptors and highly implicated in cancers and neurological disorders. Here, we report the high resolution cryo-EM structure of full-length human SSTR2 bound to the agonist somatostatin (SST-14) complex with inhibitory G (Gi) proteins. Our structure shows that seven transmembrane helices form a deep pocket for ligand binding and that the highly conserved Trp-Lys motif of SST-14 positions at the bottom of the pocket. Furthermore, our sequence analysis combined with AlphaFold modeled structures of other SSTR isoforms provide how SSTR family proteins specifically interact with their cognate ligands. This work provides the first glimpse into the molecular recognition of somatostatin receptor and crucial resource to develop therapeutics targeting somatostatin receptors.

biophysics↗
bioRxiv2020

High-density Neural Recordings from Feline Sacral Dorsal Root Ganglia with Thin-film Array

Objective: Dorsal root ganglia (DRG) are promising sites for recording sensory activity. Current technologies for DRG recording are stiff and typically do not have sufficient site density for high-fidelity neural data techniques. Approach: In acute experiments, we demonstrate single-unit neural recordings in sacral DRG of anesthetized felines using a 4.5 m-thick, high-density flexible polyimide microelectrode array with 60 sites and 30-40 m site spacing. We delivered arrays into DRG with ultrananocrystalline diamond shuttles designed for high stiffness affording a smaller footprint. We recorded neural activity during sensory activation, including cutaneous brushing and bladder filling, as well as during electrical stimulation of the pudendal nerve and anal sphincter. We used specialized neural signal analysis software to sort densely packed neural signals. Main results: We successfully delivered arrays in five of six experiments and recorded single-unit sensory activity in four experiments. The median neural signal amplitude was 55 V peak-to-peak and the maximum unique units recorded at one array position was 260, with 157 driven by sensory or electrical stimulation. In one experiment, we used the neural analysis software to track eight sorted single units as the array was retracted ~500 m. Significance: This study is the first demonstration of ultrathin, flexible, high-density electronics delivered into DRG, with capabilities for recording and tracking sensory information that are a significant improvement over conventional DRG interfaces.

bioengineering↗
bioRxiv2019

NFATC4 Promotes Quiescence and Chemotherapy Resistance in Ovarian Cancer

Development of chemotherapy resistance is a major problem in ovarian cancer. One understudied mechanism of chemoresistance is the induction of quiescence, a reversible non-proliferative state. Unfortunately, little is known about regulators of quiescence. Here we identify the master transcription factor NFATC4 as a regulator of quiescence in ovarian cancer. NFATC4 is enriched in ovarian cancer stem-like cells (CSC) and correlates with decreased proliferation and poor prognosis. Treatment of cancer cells with cisplatin results in NFATC4 nuclear translocation and activation of NFATC4 pathway, while inhibition of the pathway increased chemotherapy response. Induction of NFATC4 activity results in a marked decrease in proliferation, G0 cell cycle arrest and chemotherapy resistance, both in vitro and in vivo. Finally, NFATC4 drives a quiescent phenotype in part via downregulation of MYC. Together these data identify that NFATC4 as a driver of quiescence and a potential new target to combat chemoresistance in ovarian cancer.

cancer biology↗
bioRxiv2019

Preexisting hippocampal network dynamics constrain optogenetically induced place fields

Neuronal circuits face a fundamental tension between maintaining existing structure and changing to accommodate new information. Memory models often emphasize the need to encode novel patterns of neural activity imposed by \"bottom-up\" sensory drive. In such models, learning is achieved through synaptic alterations, a process which potentially interferes with previously stored knowledge 1-3. Alternatively, neuronal circuits generate and maintain a preconfigured stable dynamic, sometimes referred to as an attractor, manifold, or schema 4-7, with a large reservoir of patterns available for matching with novel experiences 8-13. Here, we show that incorporation of arbitrary signals is constrained by pre-existing circuit dynamics. We optogenetically stimulated small groups of hippocampal neurons as mice traversed a chosen segment of a linear track, mimicking the emergence of place fields 1,14,15, while simultaneously recording the activity of stimulated and non-stimulated neighboring cells. Stimulation of principal neurons in CA1, but less so CA3 or the dentate gyrus, induced persistent place field remapping. Novel place fields emerged in both stimulated and non-stimulated neurons, which could be predicted from sporadic firing in the new place field location and the temporal relationship to peer neurons prior to the optogenetic perturbation. Circuit modification was reflected by altered spike transmission between connected pyramidal cell - inhibitory interneuron pairs, which persisted during post-experience sleep. We hypothesize that optogenetic perturbation unmasked sub-threshold, pre-existing place fields16,17. Plasticity in recurrent/lateral inhibition may drive learning through rapid exploration of existing states.

neuroscience↗