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Kim, Y.-H.

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

At least 19 recordsLinked to original sources
bioRxiv2026

Value and spatial preferences guide habitual reaching and manual object selection in primates

Habits are automatic actions shaped by prior experience, enabling efficient and fast responses in stable environments. While habitual gaze rapidly directs the eyes toward valuable objects, the mechanisms underlying habitual manual choice for reaching and grasping remain unclear. Here we show that macaque monkeys develop habitual manual choices toward previously rewarded objects through multi-day object-value learning, driven by learned value and spatial preferences. This reaching habit persisted without reward and showed shorter latencies than in value-deliberative tasks, consistent with automatic control. Regression analyses further revealed that manual choice was guided by learned object values, whereas visual salience had no effect, unlike gaze habits. Instead, intrinsic spatial preferences continued to bias reaching behavior even after long-term value learning. These findings demonstrate that habitual manual choice arises from the integration of spatial preferences and long-term value memory, defining a distinct mechanism of automatic behavior beyond habitual gaze.

animal behavior and cognition↗
bioRxiv2026

Decoupled ionic and particulate clearance pathways determine the in vivo fate of a synthetic nanoclay-BMP-2 biomaterial during ectopic bone induction.

Nanoclay-based biomaterials offer promise for localised growth factor presentation, yet their in vivo degradation, clearance, and systemic fate remain poorly defined. Here, we investigate the fate of a synthetic nanoclay-BMP-2 gel during ectopic bone induction using a combination of in vivo imaging, histology, and component-resolved elemental analysis. Fluorescent tracking confirmed prolonged localisation of BMP-2 within the nanoclay gel and robust bone induction despite negligible growth-factor release. Inductively coupled plasma mass spectrometry (ICP-MS) revealed divergent clearance kinetics for lithium and silicon, structurally distinct components of the clay crystalline lattice, indicating decoupled ionic and particulate degradation pathways. Early clearance was dominated by cell-mediated fragmentation and the transport of clay particulates, while later stages involved preferential lithium release associated with local clay dissolution as well as integration within newly formed bone. Systemic biodistribution analysis demonstrated rapid, transient lithium release into circulation with renal clearance, contrasted with initial hepatic and then later-phase renal handling of silicon species. Together, these findings define a multiphasic in vivo clearance model for nanoclay biomaterials consistent with progressive remodelling, localised BMP-2 activity and, importantly, safe systemic handling. This work provides mechanistic insight into the activity and clearance of nanoclay-based regenerative therapies and establishes the importance of component-resolved tracking for evaluating the biodistribution of degradable inorganic biomaterials.

bioengineering↗
bioRxiv2026

ADAR-Sense: an open-access, species-agnostic web tool for automated, user-customisable ADAR-based RNA sensor design

BackgroundEngineered synthetic RNAs enable cellular control by sensing and responding to intracellular biomolecules. Recently developed sense-edit-switch RNAs (sesRNAs) based on Adenosine Deaminase Acting on RNA (ADAR)--which edits a stop codon to switch on custom payload translation in the presence of a target RNA--are consistently functional across different species. The ability of sesRNAs to couple bespoke payload translation to the presence of cell type-specific transcripts will usher in an era of precise cell-targeted biotechnological interventions. ResultsTo expedite the generation of sesRNAs, we develop ADAR-Sense--a universal web tool for automated sensor design based on user-defined sensor length, sensor-target RNA mismatch number, mismatch proximity to the ADAR-editable stop codon, and targeted custom element inclusion for improved ADAR recruitment and subsequent payload induction. ConclusionsCompared to current tools, the simplicity and flexibility of ADAR-Sense will streamline the design and screening of sesRNAs in new cell types and conditions, supporting the swift adoption of this sensing platform in both basic and translational research.

synthetic biology↗
bioRxiv2026

Quantitative Optimization of Sensitivity and Specificity in Targeted and Whole-Exome Sequencing Using Reference-Standard DNA Mixtures

BackgroundWe previously developed a benchmarking strategy using mixtures of homozygote and heterozygote DNAs as reference standards to simultaneously assess sensitivity and false positive (FP) error rates in targeted next-generation sequencing (T-NGS) and whole-exome sequencing (WES), revealing substantial variability across commercial platforms. However, optimal analytic conditions for clinical application remain undefined. MethodsWe systematically evaluated multiple sequencing kits and bioinformatics pipelines across various variant allele fraction (VAF) thresholds to identify conditions that maximize both sensitivity and specificity. Recurrent error-prone alleles were defined and filtered to enhance specificity. ResultsOptimal performance was achieved using the DRAGEN pipeline with recurrent FP allele filtering. For T-NGS, a 1% VAF cutoff yielded a 95% detection threshold of 2.99% and 1.21 FPs per megabase (FP/Mb); for WES, a 2% cutoff yielded a 95% threshold of 5.02% and 1.15 FP/Mb. These settings improved sensitivity >3-fold and reduced FP rates >96% versus suboptimal pipelines. Notably, VAF thresholds flattened sensitivity differences across platforms, obscuring key performance disparities--challenging assumptions that T-NGS is inherently more sensitive than WES. In-house and conventional pipelines undercalled up to 10% of true variants. Restricting reporting of 1-4% VAF variants to [~]1,000 predefined actionable sites enabled recovery of clinically relevant mutations while reducing FP risk >99%. ConclusionsThis study provides a quantitative framework for optimizing NGS performance. Our findings support actionable strategies to improve diagnostic accuracy in clinical genomics through tailored pipeline selection, VAF thresholding, and artifact filtering.

bioinformatics↗
bioRxiv2025

Optimizing twin prime editing components for scalable genome editing and therapy in spinocerebellar ataxia type 3

Recent advances in prime editing technologies using CRISPR modules fused with reverse transcriptase (RT) have enabled efficient and precise reprogramming of target genomic sequences. Twin prime editing using two coordinated prime editor complexes is a promising strategy for inducing extensive genomic modifications via reverse transcribed complementary templates. However, current twin prime editing systems still require improvements in editing efficiency, accuracy, and intended edit predictability. Here, efficiency and precision of twin prime editing were enhanced via engineering and optimizing conventional SpCas9(H840A)-RT-based prime editor components. A La domain-fused prime editor (La-SpCas9(H840A)-RT) and optimized pegRNAs were developed, achieving a 1.75 {+/-} 0.21-fold increase in gene editing efficiency at multiple genomic loci in human-derived cell lines without increasing off-target activity. La-SpCas9(H840A)-RT facilitated efficient [~]2.8 kb GFP transgene knock-in at target loci and eliminated the expanded polyQ tract in ATXN3 in patient-derived mutant cell lines modeling spinocerebellar ataxia type 3. The advanced twin prime editing platform expands genome engineering capabilities beyond existing CRISPR-based systems and holds great promise for diverse biotechnological and therapeutic applications.

bioengineering↗
bioRxiv2025

IFN-gamma-Induced Intestinal Epithelial Cell-Type-Specific Programmed Cell Death: PANoptosis and Its Modulation in Crohn's Disease

Crohns disease (CD) is a chronic inflammatory bowel disease (IBD) and is considered a Th1-mediated disease, supported by the over-expression of interferon-gamma (IFN-{gamma}) in the intestinal lamina propria. To evaluate the response of intestinal epithelial cells (IECs) to IFN-{gamma}, we established small intestinal organoids (enteroids) derived from non-IBD controls and CD patients. IFN-{gamma} stimulated programmed cell death (PCD) of IECs in both control and CD enteroids in a dose-dependent manner. Pyroptosis, apoptosis and necroptosis were activated in enteroids, suggesting that PANoptosis was the main process of IFN-{gamma}-induced PCD in IECs. The response to IFN-{gamma} depends on the cell type of the IECs. IFN-{gamma} induced depletion of enterocytes with upregulation of PANoptosis-associated genes, while leading to expansion of goblet cells without significant change in PANoptosis-associated gene expression. Individual PCD inhibitors were insufficient to block IFN-{gamma}-induced cytotoxicity, whereas the selective JAK1 inhibitor (upadacitinib) effectively blocked IFN-{gamma}-induced cytotoxicity and PANoptosis. Furthermore, PANoptosis was significantly activated in surgically resected tissues and in publicly available single-cell RNA-sequencing datasets of intestinal tissues from patients with CD. In conclusion, IFN-{gamma} induces PANoptosis in enterocytes, which can be treated with a selective JAK1 inhibitor in patients with CD.

cell biology↗
bioRxiv2024

Evaluation of false positive and false negative errors in targeted next generation sequencing

BackgroundAlthough next generation sequencing (NGS) has been adopted as an essential diagnostic tool in various diseases, NGS errors have been the most serious problem in clinical implementation. Especially in cancers, low level mutations have not been easy to analyze, due to the contaminating normal cells and tumor heterozygosity. ResultsIn targeted NGS (T-NGS) analyses for reference-standard samples containing mixtures of homozygote H. mole DNA with blood genomic DNA at various ratios from four certified NGS service providers, large differences in the lower detection limit of variants (16.3 times, 1.51[~]24.66%) and the false positive (FP) error rate (4280 times, 5.814 x 10-4 [~]1.359 x 10-7) were found. Employment of the commercially available Dragen system for bioinformatic analyses reduced FP errors in the results from companies BB and CC, but the errors originating from the NGS raw data persisted. Bioinformatic conditional adjustment to increase sensitivity (less than 2 times) led to a much higher FP error rate (610[~]8200 times). In addition, problems such as biased preferential reference base calls during bioinformatic analysis and high-rate FN errors in HLA regions were found in the NGS analysis. ConclusionT-NGS results from certified NGS service providers can be quite various in their sensitivity and FP error rate, suggesting the necessity of further quality controls for clinical implementation of T-NGS. The present study also suggests that mixtures of homozygote and heterozygote DNAs can be easily employed as excellent reference-standard materials for quality control of T-NGS.

genomics↗
bioRxiv2023

Human bone tissue-derived ECM hydrogels: Controlling physicochemical, biochemical, and biological properties through processing parameters

Decellularized tissues offer significant potential as biological materials for tissue regeneration due to their ability to preserve the complex compositions and architecture of the native extracellular matrix (ECM). While the use of decellularized ECM hydrogels from bovine and porcine bone tissues has been extensively studied, the evaluation and derivation of decellularized matrices from human bone tissue remain largely unexplored. The objective of this study was to investigate how the physiochemical and biological properties of ECM hydrogels derived from human bone ECM could be controlled by manipulating bone powder size (45-250 m, 250-1000 m, and 1000-2000 m) and ECM composition through modulation of digestion time (3, 5, and 7 days). The current studies demonstrate that a reduction in material bone powder size and an increase in ECM digestion time resulted in enhanced protein concentrations in the ECM hydrogels, accompanied by the presence of a diverse array of proteins. Furthermore, these adjustments in the physicochemical properties generated improved gelation strength of the hydrogels. The evaluation of human bone marrow-derived stromal cells (HBMSCs) cultured on ECM hydrogels derived from 45-250 m bone powder, treated for 7 days, demonstrated enhanced osteogenic differentiation compared to hydrogels derived from both larger bone powders and collagen gels. In conclusion, this study highlights the significant promise of human bone ECM hydrogels as biologically active materials for bone regeneration. The ability to manipulate digestion time and bone powder size enables the generation of hydrogels with enhanced release of ECM proteins and appropriate gelation and rheological properties, offering new opportunities for application in bone tissue engineering.

bioengineering↗
bioRxiv2023

Biofabrication of nanocomposite-based scaffolds containing human bone extracellular matrix for the differentiation of skeletal stem and progenitor cells

Autograft or metal implants are routinely used in skeletal repair but can fail to provide a long-term clinical resolution, emphasising the need for a functional biomimetic tissue engineering alternative. An attractive sustainable opportunity for tissue regeneration would be the application of human bone waste tissue for the synthesis of a material ink for 3D bioprinting of skeletal tissue. The use of human bone extracellular matrix (bone-ECM) offers an exciting potential for the development of an appropriate micro-environment for human bone marrow stromal cells (HBMSCs) to proliferate and differentiate along the osteogenic lineage. Extrusion-based deposition was mediated by the blending of human bone-ECM (B) with nanoclay (L, Laponite(R)) and alginate (A) polymer, to engineer a novel material ink (LAB). The inclusion of nanofiller and polymeric material increased the rheological, printability, and drug retention properties and, critically, the preservation of HBMSCs viability upon printing. The composite human bone-ECM-based 3D constructs containing vascular endothelial growth factor (VEGF) enhanced vascularisation following implantation in an ex vivo chick chorioallantoic membrane (CAM) model. Addition of bone morphogenetic protein-2 (BMP-2) with HBMSCs further enhanced vascularisation together with mineralisation after only 7 days. The current study demonstrates the synergistic combination of nanoclay with biomimetic materials, (alginate and bone-ECM) to support the formation of osteogenic tissue both in vitro and ex vivo and offers a promising novel 3D bioprinting approach to personalised skeletal tissue repair. Graphical AbstractEngineering nanoclay-based bone ECM novel bioink for bone regeneration. Human bone trabecular tissue was demineralised, decellularised and blended with nanoclay (Laponite(R)) and alginate after digestion. The resulting ink was investigated for printability following rheological and filament fusion investigation. The microstructural arrangement of the blends was examined together with viability and functionality of bioprinted HBMSCs. Finally, the ability of the novel blend to support drug release ex vivo in a CAM model was determined confirming the potential of the bone ECM ink to support bone formation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=191 SRC="FIGDIR/small/536074v1_ufig1.gif" ALT="Figure 1"> View larger version (64K): org.highwire.dtl.DTLVardef@b9dc13org.highwire.dtl.DTLVardef@1f6f0dorg.highwire.dtl.DTLVardef@1b3c098org.highwire.dtl.DTLVardef@295192_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗
bioRxiv2022

Circadian reprogramming of adipose progenitor cells regulates intermittent fasting-mediated adipose tissue remodeling and metabolic improvement

White adipose tissue (WAT) fibrosis is a hallmark of dysfunctional WAT that is directly linked to metabolic abnormalities. Recent studies have highlighted the role of dysfunctional adipose progenitor cells (APCs) in WAT fibrosis and impaired adaptive tissue plasticity, leading to systemic insulin resistance. However, therapeutic options for WAT fibrosis are limited. Intermittent fasting (IF) is an effective dietary regimen for weight control and metabolic improvement through various mechanisms, including healthy remodeling of WAT. However, whether IF is effective in improving age-associated WAT fibrosis and metabolic homeostasis is unknown. Here, we show that IF confers therapeutic benefits in aged and obese mice through reduction of WAT fibrosis. Single-cell analyses revealed that IF significantly reduces pro-fibrotic signatures within APCs along with upregulation of the circadian pathways, suggesting that the circadian clock of APCs mediates IF-induced WAT remodeling. Importantly, mice lacking core circadian gene exhibited increased fibrotic signatures in WAT and diminished beneficial response to IF, further supporting the importance of circadian rhythm in IF-mediated metabolic benefits. Lastly, insulin resistance in humans also presented with dysregulated circadian rhythm signatures in APC populations. Collectively, our findings highlight the novel role of the APC circadian rhythm in plasticity of WAT and metabolic response to IF.

molecular biology↗
bioRxiv2022

Cardiac-Gated Spectroscopic Photoacoustic Imaging for Ablation-Induced Necrotic Lesion Visualization: In Vivo Demonstration in a Beating Heart

Radiofrequency (RF) ablation is a minimally invasive therapy for heart arrhythmia, including atrial fibrillation (A-fib), which creates lesions using an electric current to isolate the heart from abnormal electrical signals. However, conventional RF procedures do not involve intraoperative monitoring of the area and extent of ablation-induced necrosis, making the assessment of the procedure completeness challenging. Previous studies have suggested that spectroscopic photoacoustic (sPA) imaging is capable of differentiating ablated tissue from its non-ablated counterpart based on PA spectrum variation. Here, we aim to demonstrate the applicability of sPA imaging in an in vivo environment, where the cardiac motion presents, and introduce a framework for mapping the necrotic lesion using cardiac-gated sPA imaging. We computed the degree of necrosis, or necrotic extent (NE), by dividing the quantified ablated tissue contrast by the total contrast from both ablated and non-ablated tissues, visualizing it as continuous colormap to highlight the necrotic area and extent. To compensate for tissue motion during the cardiac cycle, we applied the cardiac-gating on sPA data, based on the image similarity. The in vivo validation of the concept was conducted in a swine model. As a result, the ablation-induced necrotic lesion at the surface of the beating heart was successfully depicted throughout the cardiac cycle through cardiac-gated sPA (CG-sPA) imaging. The results suggest that the introduced CG-sPA imaging system has great potential to be incorporated into clinical workflow to guide ablation procedures intraoperatively.

bioengineering↗
bioRxiv2022

A Nematode-Selective Potentiator of Organophosphate and Carbamate Agrochemicals

Nematode parasites of humans, livestock and crops pose a significant burden on human health and welfare. Alarmingly, parasitic nematodes of animals have rapidly evolved resistance to anthelmintic drugs, and traditional nematicides that protect crops are facing increasing restrictions because of poor phylogenetic selectivity. Here, we present a pipeline that exploits multiple motor outputs of the model nematode C. elegans for nematicide discovery. This pipeline yielded multiple compounds that selectively kill and/or immobilize diverse nematode parasites. We focus on one compound that induces violent convulsions and paralysis that we call Nementin. We find that Nementin agonizes neuronal dense core vesicle release, which in turn agonizes cholinergic signaling. Consequently, Nementin synergistically enhances the potency of widely-used non-selective acetylcholinesterase inhibitors (AChEIs), but in a nematode-selective manner. Nementin therefore has the potential to reduce the environmental impact of toxic AChEI pesticides used to control nematode infections and infestations. Significance StatementParasitic nematodes pose a considerable burden to human health and food security. Small molecules that have traditionally been used to control these parasites have either been banned because of toxicity concerns or are being rendered ineffective because of the evolution of resistance. Significant gaps in our nematicidal toolkit are therefore becoming an alarming problem. Here, we describe our discovery of Nementin, a small molecule that disrupts the nematode nervous system but is ineffective against non-targeted organisms. We find that Nementin also enhances the activity of non-selective pesticides but does so in a nematode-selective manner. Hence, Nementin is an innovative solution to combat parasitic nematodes in a safe and phylum-selective manner. One-Sentence SummaryA C. elegans-based screening pipeline identifies a selective nematicide that also potentiates acetylcholinesterase inhibitors.

pharmacology and toxicology↗
bioRxiv2021

Highly specific chimeric DNA-RNA guided genome editing with enhanced CRISPR-Cas12a system

The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas12a system is composed of a Cas12a effector that acts as a deoxyribonucleic acid (DNA)-cleaving endonuclease and a crispr ribonucleic acid (crRNA) that guides the effector to the target DNA. It is considered a key molecule for inducing target-specific gene editing in various living systems. Here, we improved the efficiency and specificity of the CRISPR-Cas12a system through protein and crRNA engineering. In particular, to optimize the CRISPR-Cas12a system at the molecular level, we used a chimeric DNA-RNA guide chemically similar to crRNA to maximize target sequence specificity. Compared to the wild type (wt)-Cas12a system, when using enhanced Cas12a system (en-Cas12a), the efficiency and target specificity improved on average by 7.41 and 7.60 times respectively. In our study, when the chimeric DNA-RNA guided en-Cas12a effector was used, the gene editing efficiency and accuracy were simultaneously increased. These findings could contribute to highly accurate genome editing, such as human gene therapy, in the near future.

biochemistry↗
bioRxiv2021

Expansion of the prime editing modality with Cas9 from Francisella novicida

Prime editing can induce a desired base substitution, insertion, or deletion in a target gene using reverse transcriptase (RT) after nick formation by CRISPR nickase. In this study, we developed a technology that can be used to insert or replace external bases in the target DNA sequence by linking reverse transcriptase to the Francisella novicida Cas 9 [FnCas9(H969A)] nickase module, which is a CRISPR-Cas9 ortholog. Using FnCas9(H969A) nickase, the targeting limitation of existing Streptococcus pyogenes Cas9 nickase [SpCas9(H840A)]-based prime editing was dramatically extended, and accurate prime editing was induced specifically for the target genes.

bioengineering↗
bioRxiv2021

Epithelial Regeneration Ability of Crohn's Disease Assessed Using Patient-Derived Intestinal Organoids

BackgroundThe intrinsic limitation of cell lines and animal models limits our understanding of epithelial regeneration capability in Crohns disease (CD). Therefore, we aimed to study epithelial regeneration ability in CD using an intestinal organoid model. Further, since tumor necrosis factor alpha (TNF) is a major proinflammatory effector during CD pathogenesis, we also investigated TNF-induced alteration of regeneration ability in CD patient-derived intestinal organoids. MethodsHuman intestinal organoids were constructed in a three-dimensional intestinal crypt culture of enteroscopic biopsy samples from control subjects and patients with CD. The epithelial regeneration ability of intestinal organoids was assessed using organoid reconstitution, 3-(4,5-dimethylthiazolyl-2)-2,5-diphenyltetrazolium bromide (MTT), 5-ethynyl-2'-deoxyuridine (EdU), and wound healing assays. ResultsEx vivo cultures of ileal crypt cells revealed that organoid formation rate of CD patients were reduced compared with that of control subjects (p <.001). CD patient-derived organoids sub-cultured for more than 6 passages showed stable organoid reconstitution and identical morphological features. The organoid constitution and MTT assay revealed that the viability of TNF-treated CD patient-derived organoids were significantly lower than that of TNF-treated control organoids (p <.05 for each). The number of EdU+ proliferative cells was significantly lower in TNF-treated CD patient-derived organoids than in TNF-treated control organoids (p <.05). The wound-healing ability of TNF-treated CD patient-derived organoids was significantly lower than that of TNF-treated control organoids (p <.001). ConclusionsThe clinical trials are disabled to settle this issue, our results indicated that the epithelial regenerative ability is impaired in patients with CD, especially in TNF-enriched condition.

cell biology↗
bioRxiv2021

Preprocessing of general stenotic vascular flow data for topological data analysis

A new analysis and classification method of vascular disease based on topological data analysis (TDA) has been proposed in [1]. The proposed method utilizes the application of persistent homology to hemodynamic variables. Particularly, 2D homology is obtained from the velocity field of the flow projected onto the unit sphere, known as so-called the S2 projection. It was shown that such homology is closely related to the degree of vascular disease. The original method was developed based on the computational fluid dynamic (CFD) solutions of the straight stenotic vessels. In this paper, we develop a preprocessing method that enables the proposed TDA method to be applied to general stenotic vessels of irregular geometry. The velocity field is subject to a coordinate transformation correcting for orientation and curved geometry. The preprocessed data is projected onto S2 and the corresponding homology is calculated. We show that this preprocessing is necessary for the proposed TDA method to be successfully applied to general types of stenotic vessels. Validation was performed on a set of clinical data including reconstructed vascular geometry with corresponding diagnostic indices.

biophysics↗
bioRxiv2020

Impaired hand dexterity function in a non-human primate model with chronic Parkinson's disease

Symptoms of Parkinsons disease (PD) caused by loss of dopaminergic neurons are accompanied by movement disorders, including tremors, rigidity, bradykinesia, and akinesia. Non-human primate (NHP) models with PD play an essential role in the analysis of PD pathophysiology and behavior symptoms. As impairments of hand dexterity function can affect activities of daily living in patients with PD, research on hand dexterity function in NHP models with chronic PD is essential. Traditional rating scales previously used in the evaluation of animal spontaneous behavior were insufficient due to factors related to subjectivity and passivity. Thus, experimentally designed applications for an appropriate apparatus are necessary. In this study, we aimed to longitudinally assess hand dexterity function using hand dexterity task (HDT) in NHP-PD models. To validate this assessment, we analyzed an alteration in Parkinsonian tremor symptoms, loss of dopaminergic neuron, and positron emission tomography (PET) imaging of dopamine transporters (DAT) in these models. HDT latency significantly increased in NHP-PD models. In addition, a significant inverse correlation between HDT and DAT was identified, but no local bias was found. The correlation with intention tremor symptoms was lower than the resting tremor. In conclusion, the evaluation of HDT may reflect behavioral symptoms of NHP-PD models. Furthermore, HDT was effectively used to experimentally distinguish intention tremors from other tremors.

neuroscience↗