Biology subjects

Yoon, K.

Publications and source records attributed to Yoon, K..

6 recordsLinked to original sources

bioRxiv2026

Long-read sequencing reveals novel mitochondrial genome variants undetected by short-read sequencing in Korean population

While long-read sequencing technologies (e.g., PacBio Revio, ONT) have revolutionized high-quality genome assembly for the human pangenome, mitochondrial genome (mtDNA) analysis still largely relies on short-read and Sanger sequencing. However, short-read sequencing often lacks the resolution required to resolve complex variations due to the unique features of mtDNA, such as high mutation rates and repetitive homopolymeric regions, which frequently lead to alignment artifacts and mapping ambiguities. To address this, we evaluated whether applying long-read sequencing to mtDNA improves analytical quality in empirical data. Through comprehensive bioinformatics analyses, we compared the performance of long-read sequencing against short-read sequencing and microarrays. Our results revealed that long-read sequencing detected the highest number of variants (n = 533), significantly outperforming both short-read sequencing (n = 525) and microarrays (n = 49). Notably, both sequencing methods provided significantly higher resolution in haplogroup assignment compared to microarrays in terms of phylogenetic depth (p < 0.05). Long-read sequencing demonstrated superior detection power, particularly for InDels. We identified two novel non-synonymous variants, including a unique InDel detected exclusively by long-read sequencing. Protein modeling and stability analysis validated that this InDel causes structural instability (RMSD > 2.0 [A],{Delta}{Delta} G = -45.21 kcal/mol). Furthermore, we confirmed that this novel InDel is shared among haplogroup A samples in both the 1000 Genomes Project ONT dataset and the Korean population, highlighting the practical implications of long-read sequencing for molecular biology and population genetics.

genomics↗

bioRxiv2026

TRPC6-Mediated Ca2+ Influx Activates MAPK and NF κB Signaling and Elicits Pro-Inflammatory and Catabolic Responses in Human Intervertebral Disc Cells

Intervertebral disc degeneration is characterized by inflammation, extracellular matrix breakdown, and neurovascular ingrowth, processes that contribute to discogenic, chronic back pain. The transient receptor potential canonical 6 (TRPC6) channel is a calcium-permeable ion channel implicated in inflammation and pain signaling in multiple tissues; however, its functional role in human disc cells remain unknown. Here, we investigated the expression, activation, and downstream consequences of TRPC6 activation using Hyp9, a pharmacological activator of TRPC6. TRPC6 transcripts were consistently detected across all donors examined (n = 17). Functional TRPC6 activation induced a rapid, dose-dependent calcium (Ca2+) influx across 0.5-100 {micro}M Hyp9. TRPC6 activation did not reduce metabolic activity or increase cytotoxicity at concentrations commonly used for in vitro TRPC6 activation. Mechanistically, TRPC6 activation induced mitogen-activated protein kinase (MAPK) and nuclear factor kappa B (NF-{kappa}B) pathways, as demonstrated by increased phosphorylation of p38 and extracellular signal-regulated kinase (ERK), degradation of the inhibitor of {kappa}B-alpha (I{kappa}B-), and increased nuclear translocation of the NF-{kappa}B p65 subunit. Downstream of these early signaling events, TRPC6 activation elicited a robust inflammatory and catabolic response with upregulation of IL-6, IL-8, COX-2, MMP-1, MMP-3, NGF, and VEGF, with corresponding increases in protein secretion. These findings identify TRPC6 as an important signaling node linking calcium influx to inflammatory, catabolic, and neuro- and angiogenesis-associated pathways in disc cells, highlighting TRPC6 as a potential therapeutic target in degenerative disc disease. HighlightsO_ST_ABSWhat are the main findings?C_ST_ABSO_LITRPC6 is endogenously expressed in human intervertebral disc cells, and its activation induces rapid calcium influx that initiates MAPK and NF-{kappa}B signaling pathways. C_LIO_LITRPC6 activation initiates a broad inflammatory and degenerative program, elevating the expression of IL-6, IL-8, COX-2, MMP-1, MMP-3, NGF, and VEGF. C_LI What are the implications of the main findings?O_LITRPC6 functions as a key upstream regulator linking calcium influx with inflammatory, matrix-degrading, and neuro-angiogenic processes central to disc degeneration and discogenic back pain. C_LIO_LIPharmacological targeting of TRPC6 may offer a novel therapeutic approach to suppress early inflammatory signaling, limit extracellular matrix breakdown, and reduce neurovascular ingrowth in degenerative disc disease. C_LI

molecular biology↗

bioRxiv2026

ProAgio, a Novel Integrin αvβ3 Targeted Cytotoxin, Suppresses Tumor Growth and Reprograms the PDAC Microenvironment

BackgroundPancreatic ductal adenocarcinoma (PDAC) is characterized by a dense, hypoxic and immune-suppressive tumor microenvironment (TME). Integrin v{beta}3-expressing cells, including endothelial and cancer-associated fibroblasts (CAFs), contribute to the development of this TME. ProAgio is a novel cytotoxin that targets integrin v{beta}3-expressing cells. ProAgio is currently in clinical trials. We have previously shown that the combination of GPH (gemcitabine, paricalcitol, and hydroxychloroquine) influences PDAC TME. Based on the overlapping mechanisms of action, we hypothesized that ProAgio could potentiate effects of GPH and enhance its anti-tumor immunity. MethodsPatient-derived xenograft (PDX) and orthotopic models of PDAC were used to assess the therapeutic activity and mechanism of action of ProAgio in combination with GPH. Immunohistochemistry was used to evaluate hypoxia, EMT and angiogenesis. Changes in the immune cells were measured with multi-parameter flow cytometry. Dynamic contrast-enhanced MRI (DCE-MRI) was used to study tumor perfusion in mice and patients (NCT06182072). FindingsProAgio potentiated the growth inhibitory effects of GPH in PDX and orthotopic models by depleting integrin {beta}3 expressing cells, leading to ECM remodeling, reduced vascular leakage, improved hypoxia, and reversed EMT. DCE-MRI showed a significant increase in tumor perfusion following ProAgio treatment in mice and patients (NCT06182072). Immune profiling revealed that the combination treatment significantly increased the infiltration of {gamma}{delta} T cells, natural killer T (NKT) cells, CD4+ effector T cells, and M1-like macrophages. Furthermore, the combination treatment reduced the expression of myofibroblastic CAFs (myCAFs), further supporting the immunomodulatory and stromal normalizing effects of GPH and ProAgio. ConclusionTargeting integrin v{beta}3 using ProAgio modulates the PDAC TME by improving perfusion, reducing hypoxia, reversing EMT, and alleviating immune suppression. ProAgio potentiates the effects of GPH therapy, which should be evaluated in future trials.

cancer biology↗

bioRxiv2025

Real-time, High-throughput Super-resolution Microscopy via Panoramic Integration

We introduce super-resolution panoramic integration (SPI), an on-the-fly microscopy technique enabling instantaneous generation of subdiffractional images concurrently with scalable, high-throughput screening. SPI leverages multifocal optical rescaling, high-content sweeping, and synchronized line-scan readout while preserving minimal post-processing and compatibility with epi-fluorescence settings. We demonstrate SPI for various subcellular and populational morphology, function, and heterogeneity. This versatile platform offers a practical pathway toward biological insights beyond traditional optical and computational constraints.

bioengineering↗

bioRxiv2024

Cell crowding induces TRPV4 inhibition and its relocation to plasma membranes, implicating pro-invasive cell volume reduction mechanotransduction pathway

Cell crowding is a common microenvironmental factor influencing various disease processes, but its role in promoting cell invasiveness remains unclear. This study investigates the biomechanical changes induced by cell crowding, focusing on pro-invasive cell volume reduction in ductal carcinoma in situ (DCIS). Crowding specifically enhanced invasiveness in high-grade DCIS cells through significant volume reduction compared to hyperplasia-mimicking or normal cells. Mass spectrometry revealed that crowding selectively relocated ion channels, including TRPV4, to the plasma membrane in high-grade DCIS cells. TRPV4 inhibition triggered by crowding decreased intracellular calcium levels, reduced cell volume, and increased invasion and motility. During this process, TRPV4 membrane relocation primed the channel for later activation, compensating for calcium loss. Analyses of patient-derived breast cancer tissues confirmed that plasma membrane- associated TRPV4 is specific to high-grade DCIS and indicates the presence of a pro-invasive cell volume reduction mechanotransduction pathway. Hyperosmotic conditions and pharmacologic TRPV4 inhibition mimicked crowding-induced effects, while TRPV4 activation reversed them. Silencing TRPV4 diminished mechanotransduction in high-grade DCIS cells, reducing calcium depletion, volume reduction, and motility. This study uncovers a novel pro-invasive mechanotransduction pathway driven by cell crowding and identifies TRPV4 as a potential biomarker for predicting invasion risk in DCIS patients.

cell biology↗

bioRxiv2019

Combined modulation of SHH and FGF signaling is crucial for maintenance of the neocortical progenitor specification program

Neuronal progenitors in the developing forebrain undergo dynamic competence states to ensure timely generation of specific excitatory and inhibitory neuronal subtypes from distinct neurogenic niches of the dorsal and ventral forebrain, respectively. Here we show evidence of progenitor plasticity when Sonic hedgehog (SHH) signaling is left unmodulated in the embryonic neocortex of the dorsal forebrain. At early stages of corticogenesis, loss of Suppressor of Fused (Sufu), a potent inhibitor of SHH signaling, in neocortical progenitors, altered their transcriptomic landscape. Ectopic activation of SHH signaling occurred, via degradation of Gli3R, resulting in significant upregulation of Fibroblast Growth Factor 15 (FGF15) gene expression. Consequently, activation of FGF signaling, and its downstream effector the MAPK signaling, facilitated expression of genes characteristic of ventral forebrain progenitors. Our studies identify the importance of modulating extrinsic niche signals such as SHH and FGF15 to maintain the competency and specification program of neocortical progenitors throughout corticogenesis. SIGNIFICANCE STATEMENTLow levels of FGF15 control progenitor proliferation and differentiation during neocortical development but little is known on how FGF15 expression is maintained. Our studies identified SHH signaling as a critical activator of FGF15 expression during corticogenesis. We found that Sufu, via Gli3R, ensured low levels of FGF15 was expressed to prevent abnormal specification of neocortical progenitors. These studies advance our knowledge on the molecular mechanisms guiding the generation of specific neocortical neuronal lineages, their implications in neurodevelopmental diseases, and may guide future studies on how progenitor cells may be utilized for brain repair.

developmental biology↗