Biology subjects

Kim, Y.-S.

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

13 recordsLinked to original sources

bioRxiv2026

Splanchnic-spinal transmission of gut-initiated α-synucleinopathy

Gut-initiated -synucleinopathy is proposed to spread from the gastrointestinal tract to the CNS, contributing to Parkinson's disease (PD), but whether routes beyond the vagus nerve are involved remains unclear. Using complementary intracolonic rotenone and gastroduodenal -synuclein PFF models, we combined pathway-specific surgical interruption with longitudinal behavioral analysis and anatomical mapping of pathological -synuclein. In the intracolonic rotenone model, interruption of the prevertebral ganglia/splanchnic-spinal axis more strongly attenuated behavioral deficits and -synuclein pathology than vagotomy. In the gastroduodenal PFF model, both vagal and splanchnic-spinal pathways contributed to pathology propagation. Early after PFF inoculation, pathological -synuclein was detected in peripheral neural structures associated with both routes. Consistent with these findings, spinal pathology was evident in human PD. Together, these results identify the splanchnic-spinal pathway as a key component of body-first Parkinson's disease, broadening current models of peripheral-to-central disease progression and informing efforts to target early peripheral disease progression.

neuroscience↗

bioRxiv2026

Wasf1 deletion attenuates tau hyperphosphorylation, microglial state transition, and cognitive deficits in P301S tau mice

We previously reported that WAVE1, a major activator of Arp2/3 complex-mediated actin polymerization, is downregulated in postmortem brains of Alzheimers disease (AD) and that WAVE1 regulates amyloid precursor protein trafficking and amyloid-{beta} production. However, its role in tau pathology remains unknown. Here, we demonstrate that WAVE1 activity is suppressed in P301S tau mice through elevated inhibitory phosphorylation. Strikingly, WAVE1 gene (Wasf1) knockout in P301S tau mice significantly reduces tau hyperphosphorylation and improves cognition, suggesting a compensatory role for WAVE1 suppression in tau pathogenesis. Single-nucleus RNA sequencing reveals that Wasf1 deletion in P301S tau mice reverses microglial state transitions, with minimal impact on other brain cell types. Wasf1 mRNA is highly translated in microglia in non-Tg mice, while its expression is downregulated in P301S tau mice. Wasf1 knockdown in BV2 microglia cells enhances the degradation of engulfed tau fibrils, indicating WAVE1 as an endogenous regulator of microglial function. Additionally, CellChat analysis indicates that Wasf1 deletion alters microglial autocrine signaling and their interactions with other cell types in P301S tau mice. These findings, taken together, suggest that Wasf1 deletion restores homeostatic microglial function, mitigates tau pathology, and alleviates cognitive deficits, highlighting WAVE1 as a potential therapeutic target for tauopathy-related dementias.

neuroscience↗

bioRxiv2025

An integrated in silico-in vitro workflow for discovering high-affinity, selective antibodies to the KRAS(G12D)-MHC I complex

Antibodies that recognize peptide-loaded class I major histocompatibility complex (pMHC I) molecules could enable therapeutic targeting of intracellular oncogenic proteins, yet their discovery has been hampered by the small size of peptide antigens and allele-specificity. We describe an integrated in silico-in vitro workflow for generating high-affinity, selective antibodies to KRAS(G12D)10 presented by HLA-C*08:02, a clinically validated cancer neoantigen. In silico, multiple human antibody-derived variable fragments (Fvs) plausibly docked to the target pMHC were generated, followed by limited complementarity-determining region (CDR) sequence design. In vitro, CDR diversity was introduced at 3-4 positions per Fv to construct yeast surface display library for iterative selections. This workflow yielded antibodies with exclusive binding to KRAS(G12D)10/HLA-C*08:02 without cross-reactivity. Affinity maturation achieved nanomolar dissociation constants, and incorporation into chimeric antigen receptor T cells enabled specific activation against target-positive cells. This study establishes a practical design-to-function pipeline for TCR-like antibody discovery, and demonstrates the feasibility of therapeutic targeting against KRAS(G12D)-driven malignancies.

biochemistry↗

bioRxiv2025

RHOV is a Detachment-Responsive Rho GTPase Necessary for Ovarian Cancer Peritoneal Metastasis

All ovarian cancer subtypes spread via transcoelomic metastasis, where cells disseminate into the peritoneal fluid, resist anoikis, and form multicellular aggregates that invade the peritoneum. This represents the main driver of morbidity and mortality for peritoneal cancer patients. Mechanisms necessary for cancer cells to survive matrix detachment and initiate transcoelomic metastasis remain poorly defined. To address this, we identified a conserved detachment-sensitive gene signature activated shortly after matrix-detachment across multiple ascites-derived cancer cell lines. RHOV, an atypical, constitutively active and understudied member of the Rho GTPase family, emerged as a top upregulated transcript, which was confirmed in patient ascites-derived tumor cells. Functionally, loss of RHOV impairs anoikis resistance, multicellular aggregate integrity, migration and invasion, and completely abolishes transcoelomic tumor progression in vivo. RHOV enhances c-Jun signaling and cytoskeletal remodeling, which is dependent on both RHOV GTP-binding and membrane localization. These findings define RHOV as a novel detachment-sensitive Rho GTPase and establish RHOV as a critical regulator of peritoneal metastasis for the first time.

cancer biology↗

bioRxiv2023

Inferring Disease Progressive Stages in Single-Cell Transcriptomics Using Weakly-Supervised Deep Learning Approach

BackgroundApplication of single-cell/nucleus genomic sequencing to patient-derived tissues offers potential solutions to delineate disease mechanisms in human. However, individual cells in patient-derived tissues are in different pathological stages, and hence such cellular variability impedes subsequent differential gene expression analyses. ResultTo overcome such heterogeneity issue, we present a novel deep learning approach, scIDST, that infers disease progressive levels of individual cells with weak supervision framework. The inferred disease progressive cells displayed significant differential expression of disease-relevant genes, which could not be detected by comparative analysis between patients and healthy donors. In addition, we demonstrated that pre-trained models by scIDST are applicable to multiple independent data resources, and advantageous to infer cells related to certain disease risks and comorbidities. ConclusionTaken together, scIDST offers a new strategy of single-cell sequencing analysis to identify bona fide disease-associated molecular features.

genetics↗

bioRxiv2021

Antiviral Effect of Hyunggaeyungyo-tang on A549 Cells Infected with Human Coronavirus

BackgroundHerbal medicine is widely recommended to treat viral infectious diseases. Over 123,000,000 individuals have been infected with the coronavirus since a worldwide pandemic was declared in March 2020. We conducted this research to confirm the potential of herbal medicine as a treatment for coronavirus. MethodsWe infected the A549 cell line with beta coronavirus OC43 then treated with 100 g/mL Hyunggaeyungyo-tang (HGYGT) or distilled water with a control of HGYGT. We measured the mRNA expression levels of pro-inflammatory cytokines and interferon stimulated genes (ISGs) to confirm the effectiveness of HGYGT upon coronavirus infection. ResultsWe found the effects of HYGYT decrease the expression level of pPKR, peIF2, IFI6, IFI44, IFI44L, IFI27, IRF7, OASL and ISG15 when administered to cells with coronavirus infection. The expressions of IL-1, TNF-, COX-2, NF-{kappa}B, iNOS and IKK mRNA were also significantly decreased in the HGYGT group than in the control group. ConclusionThrough the reduction of the amount of coronavirus RNA, our research indicates that HGYGT has antiviral effects. The reduction of IKK and iNOS mRNA levels indicate that HGYGT reduces coronavirus RNA expression and may inhibits the replication of coronavirus by acting on NF-kB/Rel pathways to protect oxidative injury. In addition, decreases in mRNA expression levels of pro-inflammatory cytokines indicate that the HGYGT may relieve the symptoms of coronavirus infections.

cell biology↗

bioRxiv2020

Detecting regulatory elements in high-throughput reporter assays

High-throughput reporter assays such as self-transcribing active regulatory region sequencing (STARR-seq) have made it possible to measure genome-wide regulatory element activity across the human genome. The assays, however, also present substantial analytical challenges. Here, we identify technical biases that explain most of the variance in STARR-seq signals. We then develop a statistical model to correct those biases and to improve detection of regulatory elements. This approach substantially improves precision and recall over current methods, improves detection of both activating and repressive regulatory elements, and controls for false discoveries despite strong local signal correlations.

bioinformatics↗

bioRxiv2020

COVID-19 patients upregulate toll-like receptor 4-mediated inflammatory signaling that mimics bacterial sepsis

Observational studies of the ongoing coronavirus disease 2019 (COVID-19) outbreak suggest that a cytokine storm is involved in the pathogenesis of severe illness. However, the molecular mechanisms underlying the altered pathological inflammation in COVID-19 are largely unknown. We report here that toll-like receptor (TLR) 4-mediated inflammatory signaling molecules are upregulated in peripheral blood mononuclear cells (PBMCs) from COVID-19 patients, compared with healthy controls. Among the most highly increased inflammatory mediators in severe/critically ill patients, S100A9, an alarmin and TLR4 ligand, was found as a noteworthy biomarker, because it inversely correlated with the serum albumin levels. These data support a link between TLR4 signaling and pathological inflammation during COVID-19 and contribute to develop therapeutic approaches through targeting TLR4-mediated inflammation.

immunology↗

bioRxiv2020

Antibiotic-dependent relationships between nasal microbiome and secreted proteome in chronic rhinosinusitis and nasal polyps

BackgroundAntibiotics are commonly prescribed to treat chronic rhinosinusitis (CRS); however, the effects of antibiotics on the microbiome and secreted proteome remain unknown in regard to CRS. ObjectiveWe analyzed the effects of antibiotics on the nasal microbiome and secreted proteome in the context of CRS using multi-omic analysis. MethodsNasal secretions were collected from 29 control, 30 CRS patients without nasal polyps (CRSsNP), and 40 CRS patients with nasal polyps (CRSwNP). A total of 99 subjects were divided into two groups that included subjects who had taken antibiotics 3 months prior to sampling (ABX) and those who had not (NABX). We performed 16S rDNA sequence analyses and Orbitrap mass spectrometry-based proteomic analyses in data-independent acquisition (DIA) on the nasal secretions. Spearman correlation was used to assess the correlations between the nasal microbiome and secreted proteome. ResultsWe observed a strong association between the nasal microbiome and secreted proteome according to disease status. Antibiotic use reduced differences in the microbial community and secreted proteome according to disease status. Interestingly, in nasal polyp (NP) patients, antibiotics exhibited strong effects not only on the nasal microbiome and the secreted proteome but also on their associations. Additionally, their correlations were strengthened in subjects who had taken antibiotics. ConclusionIntegrative analyses revealed that the correlations between the microbiome and the secreted proteome could be altered and strengthened in subjects who used antibiotics. These findings provide novel insight into the effects of antibiotics on the nasal environment and the host responses in CRS.

microbiology↗

bioRxiv2020

Targeted attenuation of elevated histone marks at SNCA alleviates α-synuclein in Parkinson's disease

Epigenetic de-regulation of -synuclein plays a key role in Parkinsons disease (PD). Analysis of the SNCA promoter using the ENCODE database revealed the presence of important histone posttranslational modifications (PTMs) including transcription-promoting marks, H3K4me3 and H3K27ac, and repressive mark, H3K27me3. We investigated these histone marks in postmortem brains of controls and PD patients and observed that only H3K4me3 was significantly elevated at the SNCA promoter of the substantia nigra (SN) of PD patients both in punch biopsy as well as in NeuN positive neuronal nuclei samples. To understand the importance of H3K4me3 in regulation of -synuclein, we developed CRISPR/dCas9-based locus-specific H3K4me3 demethylating system where the catalytic domain of JARID1A was recruited to the SNCA promoter. This CRISPR/dCas9 SunTag-JARID1A significantly reduced H3K4me3 at SNCA promoter and concomitantly decreased -synuclein both in the neuronal cell line SH-SY5Y and idiopathic PD-iPSC derived dopaminergic neurons. In sum, this study indicates that -synuclein expression in PD is controlled by SNCAs histone PTMs and modulation of the histone landscape of SNCA can reduce -synuclein expression.

neuroscience↗

bioRxiv2019

Polarized Lung Inflammation and Tie2/Angiopoietin-Mediated Endothelial Dysfunction during Severe Orientia tsutsugamushi Infection

Orientia tsutsugamushi infection can cause acute lung injury and high mortality in humans; however, the underlying mechanisms are unclear. Here, we tested a hypothesis that dysregulated pulmonary inflammation and Tie2-mediated endothelial malfunction contribute to lung damage. Using a murine model of lethal O. tsutsugamushi infection, we demonstrated pathological characteristics of vascular activation and tissue damage: 1) a significant increase of ICAM-1, VEGFR2, and angiopoietin-2 (Ang2) proteins in inflamed tissues and lung-derived endothelial cells (EC), 2) a progressive loss of endothelial quiescent and junction proteins (Ang1, VE-cadherin/CD144, occuludin), and 3) a profound impairment of Tie2 receptor at the transcriptional and functional levels. In vitro infection of primary human EC cultures and serum Ang2 proteins in scrub typhus patients support our animal studies, implying endothelial dysfunction in severe scrub typhus. Flow cytometric analyses of lung-recovered cells further revealed that pulmonary macrophages (M{Phi}) were polarized toward an M1-like phenotype (CD80+CD64+CD11b+Ly6G-) during the onset of disease and prior to host death, which correlated with the significant loss of CD31+CD45- ECs and M2-like (CD206+CD64+CD11b+Ly6G-) cells. In vitro studies indicated extensive bacterial replication in M2-type, but not M1-type, M{Phi}s, implying the protective and pathogenic roles of M1-skewed responses. This is the first detailed investigation of lung cellular immune responses during acute O. tsutsugamushi infection. It uncovers specific biomarkers for vascular dysfunction and M1-skewed inflammatory responses, highlighting future therapeutic research for the control of this neglected tropical disease.\n\nAuthor SummaryScrub typhus is a life-threatening disease, infecting an estimated one million people yearly. Acute lung injury is the most common clinical observation; however, its pathogenic biomarkers and mechanisms of progression remain unknown. Here, we used a lethal infection mouse model that parallels certain aspects of severe scrub typhus, primary human endothelial cell cultures, and patient sera to define pathogenic biomarkers following Orientia tsutsugamushi infections. We found a significant increase in the levels of endothelial activation/stress markers (angiopoietins and ICAM-1) in infected mouse lungs and in patient sera, but a progressive loss of endothelium-specific Tie2 receptor and junction proteins (VE-cadherin), at severe stages of disease. These signs of vasculature disruption positively correlated with the timing and magnitude of recruitment/activation of proinflammatory M{Phi} subsets in infected lungs. Bacterial growth in vitro was favored in M2-like, but not in M1-like, M{Phi}s. This study, for the first time, reveals endothelial malfunction and dysregulated inflammatory responses, suggesting potential therapeutic targets to ameliorate tissue damage and pathogenesis.

microbiology↗

bioRxiv2019

Synthetic lethality targeting LKB1 mutant and EGFR wild type human non-small cell lung cancer cells by glucose starvation and SGLT2 inhibition

In this study, we aimed to discover novel therapeutic approaches targeting non-small cell lung cancer (NSCLC) patients without EGFR mutation. First, we found that mutations of EGFR and LKB1 are mutually exclusive in NSCLC. EGFR-WT/LKB1-mutant cells are resistant to EGFR inhibitor erlotinib but are highly susceptible to glucose starvation or SGLT2 inhibitor canagliflozin. Mechanistically, in these cells, glucose starvation causes suppression of AMPK and induction of oxidative stress, leading to cell death. Finally, canagliflozin effectively reduces tumor growth of EGFR-WT/LKB1-mutant NSCLC cells in the mice xenograft model. Our data thus demonstrate that synthetic lethality can be achieved by glucose starvation or SGLT2 inhibition in EGFR-WT/LKB1-mutant NSCLC.\n\nSIGNIFICANCEAt present, EGFR inhibitor-based targeted therapy can only benefit those non-small cell lung cancer (NSCLC) patients with EGFR mutation. Therefore, there is an urgent need to develop alternate targeted therapy for NSCLC with WT EGFR. In this study, we found that mutations of EGFR and LKB1 are mutually exclusive in NSCLC, and more importantly, synthetic lethality can be achieved in EGFR-WT/LKB1-mutant NSCLC cells with glucose starvation or SGLT2 inhibition. Since SGLT2 inhibitors such as canagliflozin are FDA-approved drugs for type II diabetes, our study thus points out a possibility of developing SGLT2 inhibitors as a targeted therapy for NSCLC patients with WT EGFR and mutant LKB1, which will benefit about 15-30% of NSCLC patients.\n\nHIGHLIGHTSO_LIEGFR and LKB1 mutations are mutually exclusive in NSCLC\nC_LIO_LIEGFR-WT/LKB1-mutant NSCLC cells are sensitive to cell death induced by glucose starvation and SGLT2 inhibition\nC_LIO_LIGlucose starvation suppresses AMPK activity in LKB1-mutant NSCLC cells\nC_LIO_LISGLT2 inhibitor canagliflozin causes synthetic lethality in LKB1-mutant NSCLC cells\nC_LI

cancer biology↗

bioRxiv2017

Endogenous α-SYN protein analysis on human brain tissues using single-molecule pull-down assay

Alpha-synuclein (-SYN) is a central molecule in Parkinsons disease pathogenesis. Despite several studies, the molecular nature of endogenous -SYN especially in human brain samples is still not well understood due to the lack of reliable methods and the limited amount of bio-specimens. Here, we introduce -SYN single-molecule pull-down (-SYN SiMPull) assay combined with in vivo protein crosslinking to count individual -SYN protein and assess its native oligomerization states from biological samples including human postmortem brains. A SiMPull assay enables us to count the number of immuno-precipitated proteins, and reveal the stoichiometry of protein complexes by single-molecule fluorescence imaging. This powerful assay can be highly useful in diagnostic applications using various specimens for neurodegenerative diseases including Alzheimers disease and Parkinsons disease.

biophysics↗