Biology subjects

Park, J.

Publications and source records attributed to Park, J..

At least 163 records · Page 9Linked to original sources

bioRxiv2025

Analysis of Microsatellite Instability Intensity in Single-Cell Resolution with scMnT reveals Tumor Heterogeneity in Colorectal Cancer

Although microsatellite instability (MSI) is traditionally regarded as a binary trait, growing evidence indicates that it exists on a continuum, with higher intensity of MSI correlating with better prognosis. However, accurate quantification of MSI intensity is challenging due to the heterogeneous cellular composition of the tumor microenvironment. To this end, we introduce scMnT, a bioinformatic method for identifying MSI cells at single-cell resolution and quantifying MSI intensity based on microsatellite allele lengths. Applying scMnT to scRNA-seq datasets produced robust results and revealed substantial variation in MSI intensity among colorectal cancer patients, with higher MSI intensity correlating with improved responses to immunotherapy. Transcriptomic analyses revealed that MSI intensity-low cancer cells were enriched in goblet signatures, whereas MSI intensity-high cancer cells exhibited strong stem cell characteristics, suggesting a potential link between MSI intensity and cancer cell origin. Our approach provides a novel framework for analyzing MSI at the single-cell level, allowing new opportunities for MSI research.

bioinformatics↗

bioRxiv2025

Hydrophobic Ion Pairing for Simple, Non-Toxic Transfection

Although biomacromolecules require intracellular delivery for therapeutic effect, existing transfection agents are often characterized by high cost, low efficiency, and/or cytotoxicity. Here, we describe a new transfection approach based on hydrophobic ion pairing (HIP), which involves the simple mixing of a hydrophobic counterion with charged biomacromolecules. Among tested cargoes (proteins, siRNA, and pDNA), the HIP siRNA system performed especially well, achieving silencing in fibroblasts (80%), T cells (90%), and neurons (70%). HIP siRNA was also highly potent in mice, with tropism dependent on the route of administration. Most notably, intraperitoneal administration enabled [~]40% LAMP-1 knockdown in the pancreas, and intravenous delivery resulted in a remarkable 80% silencing in the heart. Heart delivery was also highly selectively, with no significant knockdown in the liver. Together, these data demonstrate a new, inexpensive approach to biomacromolecular delivery with the potential to target difficult-to-transfect organs, thus expanding the therapeutic potential of nucleic acids.

bioengineering↗

bioRxiv2025

Interventionally targeting somatic CAG expansions can be a rapid disease-modifying therapeutic avenue: Preclinical evidence.

Huntington disease (HD) is caused by inherited CAG expansions, which continue expanding somatically in affected brain regions to hasten disease onset and progression. Therapeutically diminishing somatic expansions is expected to be clinically beneficial. However, it is not known if interventionally modifying somatic CAG expansions will actually modify in vivo clinically-relevant phenotypes, what the therapeutic window is, or which phenotypes will be altered. Here we show that acute (6-week) delivery of the contraction-inducing slipped-CAG DNA ligand naphthyridine-azaquinolone to young (4-week-old) (CAG)120 HD mice, induces contractions throughout brain regions, improves motor function (locomotion, balance, coordination, muscle strength), molecular disease landmarks (mHTT aggregates, nuclear envelope morphology, nucleocytoplasmic mRNA transport, transcriptomic dysregulation, neuroinflammation), and neurodegeneration. Beneficial effects of modifying somatic expansions were also evident in muscle and blood, where blood CAG instability correlated with brain instability and blood serum had diminished levels of neurofilament light (a biomarker for neurodegeneration) -- offering blood as having elements of target engagement and efficacy. These data support that targeting somatic repeat expansions can be a rapid disease-modifying therapeutic avenue for HD and possibly other repeat expansion diseases. Our findings support an etiologic pathway interconnected to somatic CAG expansions that will inform the design of clinical trials expecting clinical benefit by modulating somatic expansions.

genetics↗

bioRxiv2025

Globally prevalent Kelch13 mutations increase partial artemisinin resistance and fitness in Bangladeshi Plasmodium falciparum parasites

Artemisinin partial resistance (ArtR), mediated by Kelch13 (K13) gene mutations in Plasmodium falciparum, has caused delayed parasite clearance and, together with partner drug resistance, treatment failures in the Greater Mekong Subregion (GMS). The Chittagong Hill Tracts (CHTs), located in southeastern Bangladesh and bordering Myanmar and India, regions with prevalent K13 mutations, account for approximately 90% of the countrys malaria infections but have not yet reported ArtR-causing K13 mutations. Importantly, however, some isolates from the CHTs have demonstrated moderate in vitro ArtR in the absence of K13 mutations. To assess the potential threat of K13-mediated ArtR in Bangladesh, we proactively evaluated the impact of three prevalent neighboring K13 mutations (F446I, R561H, and C580Y) on ArtR and parasite fitness in parasites isolated from the CHTs. We edited these mutations into two distinct genetic backgrounds: an artemisinin-sensitive strain (CHT-S) and a K13-independent, moderately resistant strain (CHT-R). In these edited lines, we then evaluated ArtR levels and fitness using ring-stage survival assays (RSA), post-drug treatment recovery assays, and competitive fitness assays against isogenic control strains. Prior to genome editing, both isolates were characterized for baseline drug susceptibility, resistance-associated mutations, and population structure. We found that C580Y and R561H mutations, but not F446I, confer increased in vitro ArtR in the CHT-R background already exhibiting K13-independent moderate resistance. All three mutations incurred minimal or no fitness costs in both genetic backgrounds. Notably, R561H, the dominant allele at the Thai-Myanmar border and currently expanding in Rwanda, mediates extreme resistance in the CHT-R background, with mean RSA survival rates of 30.9{+/-}1.9%, an unprecedented resistance level among K13-engineered lines. R561H also showed fitness advantages (0.5% per generation) and the highest growth recovery post-treatment. This represents the first experimental study modeling this K13 mediated ArtR risk in Bangladeshi parasites. In conclusion, we found that indigenous P. falciparum isolates in the CHTs possess inherent genetic potential to sustain high-level ArtR and fitness advantages if K13 mutations emerge, raising urgent concerns for containment and surveillance strategies during Bangladeshs malaria elimination phase.

microbiology↗

bioRxiv2025

Ophiobolin A selectively alters mitochondria, metabolism and redox biology in breast cancer and mammary epithelial cells which have undergone epithelial to mesenchymal transition

Breast cancer progression is facilitated by the epithelial to mesenchymal transition (EMT), generating cancer cells with enhanced metastatic capacity and resistance to chemotherapeutics. EMT is known to impart changes in metabolic pathways and mitochondrial function. Here, we show a natural product possesses EMT-specific cytotoxic activity via alterations in metabolic and mitochondrial functions. The fungus-derived sesterterpenoid, ophiobolin A (OpA), possesses nanomolar cytotoxic activity and a high therapeutic index, although its target and mechanism of action remain unknown. Here, we utilized a model of mammary epithelial cells and breast cancer cell lines with and without EMT features to characterize the mechanism of selectivity towards EMT(+) cells by OpA and to identify novel targets for the treatment of EMT-enriched breast cancer. Proteins interacting with OpA in EMT(+) cells were identified through proteomic studies. We utilized trans-mitochondrial cybrids to determine that mitochondria mediate sensitivity to OpA. Furthermore, we report effects on glycolysis, oxidative metabolism, and disruption of metabolite abundance in the TCA cycle. Alterations to mitochondrial iron concentrations and glutathione production, mediated partly by OpA engagement with the metabolic proteins CISD3 and SLC25A40, were also detected in EMT(+) cells. Antioxidant mechanisms are activated by OpA in EMT(+) cells via the NRF2-ARE pathway, verified by decreased cytotoxicity in EMT(+) cells pretreated with the NRF2 activator CDDO. Collectively, we conclude that OpA selectivity toward EMT is mediated by the mitochondria, and at sub-cytotoxic levels, generates a metabolic shift leading to cell death countered by antioxidant mechanisms.

cancer biology↗

bioRxiv2025

A gel-top model for characterizing mesenchymal features of glioblastoma cells

Glioblastoma (GBM) remains one of the most aggressive adult cancers, with limited treatment options due to an incomplete understanding of its biology. GBM exhibits different transcriptional subtypes, among which the mesenchymal (mGBM) variant is associated with a particularly aggressive nature and poor outcomes. Developing models that capture mGBM phenotypes could offer new insights into its biology and therapeutic vulnerabilities. However, the lack of in vitro models for mGBM has posed challenges in investigating the aggressive GBM subtype. Here, we present a gel-top culture model in which GBM cells exhibit MES features, including distinct transcriptomic profiles, invasive phenotypes, cell morphology, and cytoskeletal organization. Furthermore, co-culturing GBM cells with microglia in this system revealed enhanced microglial recruitment and interaction, effectively recapitulating the tumor microenvironment of mGBM that traditional 2D culture fails to model. Using the bioinformatic tool, Small Molecule Suite, we identified casein kinase 2 (CK2) as a targetable molecule in GBM cells within our system, potentially driving MES features. Notably, CK2 inhibitors reduced the mesenchymal signature of mGBM cells, suggesting their potential as a targeted therapy for mGBM. Together, our findings suggest that the gel-top culture model replicates key features of mGBM, serving as a valuable platform for studying its biology and identifying novel therapeutic strategies.

bioengineering↗

bioRxiv2025

Quantifying Uncertainty in Phasor-Based Time-Domain Fluorescence Lifetime Imaging Microscopy

The phasor approach to time-domain fluorescence lifetime imaging microscopy (FLIM) offers a powerful, fit-free method for analyzing complex fluorescence decay signals. However, its quantitative accuracy is fundamentally limited by noise--particularly photon shot noise--which introduces variability and bias in lifetime estimation and fluorophore unmixing. In this study, we present a theoretical uncertainty model for phasor-based time-domain FLIM that analytically captures the propagation of shot noise and quantifies its impact on phasor coordinates and fluorophore weight estimation. We validate the model using Monte Carlo simulations and experimental data acquired from standard fluorescent dyes and biological tissue samples. Our model improves the overall reliability and efficiency of phasor-based time-domain FLIM, particularly in photon-limited imaging applications.

bioinformatics↗

bioRxiv2025

A proteogenomic tool uncovers protein markers for human microglial states

Human microglial heterogeneity has been largely described using transcriptomic data. Here, we introduce a microglial proteomic data resource and a Cellular Indexing of Transcriptomes and Epitopes by Sequencing panel enhanced with antibodies targeting 17 microglial cell surface proteins (mCITE-Seq). We evaluated mCITE-Seq on HMC3 microglia-like cells, induced-pluripotent stem cell-derived microglia (iMG), and freshly isolated primary human microglia. We identified novel protein microglial markers such as CD51 and relate expression of 101 cell surface proteins to transcriptional programs. This results in the identification and validation of three protein marker combinations with which to purify microglia enriched with each of 23 transcriptional programs; for example, CD49D, HLA-DR and CD32 enrich for GPNMBhigh ("disease associated") microglia. Further, we identify and validate proteins - SIRPA, PDPN and CD162 - that differentiate microglia from infiltrating macrophages. The mCITE-Seq panel enables the transition from RNA-based classification and facilitates the functional characterization and harmonization of model systems.

neuroscience↗

bioRxiv2025

A guide for Single Particle Tracking: from sample preparation and image acquisition to the analysis of individual trajectories

Live-cell Single-Particle Tracking (SPT) is a powerful super resolution microscopy approach. It allows us to observe live recordings of individual molecules in living cells at high temporal and spatial resolution (100 Hz, 20 nm). Here, we discuss the implementation and application of super-resolution microscopy to quantify the mobility of single molecules in living human cells. We first describe the human cell sample preparation for SPT with an experimental time line overview, then super-resolution microscope setting and procedure to acquire SPT films for further SPT video analyses. We provide a practical guide to determine the quality of acquired SPT films in particular, number of photons and fluorescent background. Furthermore, we introduce several SPT video analysis software comparing their advantages and limitations. Expectantly, this SPT protocol will serve as a foundation for a better SPT performance.

biophysics↗

bioRxiv2025

Tonotopic Specialization of MYO7A Isoforms in Auditory Hair Cells

1.Mutations in Myo7a cause Usher syndrome type 1B and non-syndromic deafness, but the precise function of MYO7A in sensory hair cells remains unclear. We identify and characterize a novel isoform, MYO7A-N, expressed in auditory hair cells alongside the canonical MYO7A-C. Isoform-specific knock-in mice reveal that inner hair cells primarily express MYO7A-C, while outer hair cells express both isoforms in opposing tonotopic gradients. Both localize to the upper tip-link insertion site, consistent with a role in the tip link for mechanotransduction. Loss of MYO7A-N leads to outer hair cell degeneration and progressive hearing loss. Cryo-EM structures reveal isoform-specific differences at actomyosin interfaces, correlating with distinct ATPase activities. These findings reveal an unexpected layer of molecular diversity within the mechanotransduction machinery. We propose that MYO7A isoform specialization enables fine-tuning of tip-link tension, thus hearing sensitivity, and contributes to the frequency-resolving power of the cochlea.

neuroscience↗

bioRxiv2025

Designed Peptides as Affinity Ligands for Extracellular-Vesicle-based Cancer Biomarker Detection

Assays for cancer diagnosis via the analysis of tumor biomarkers on circulating extracellular vesicles (EVs) have shown great potential. Single EV imaging that can measure the abundance of protein biomarkers in EVs can help in detecting the presence, stage, and progression of disease. Antibodies are typically used to detect EV proteins. Controlling the quality of antibody-based immunoassays can, however, be challenging, as they may exhibit unintended cross-reactivity with non-target proteins or variability in binding affinity across different batches, even for monoclonal antibodies. Here, we report short peptides that are a promising alternative to antibodies for detecting protein biomarkers in EVs. We describe an effort that combines a Peptide Binding Design (PepBD) algorithm and molecular-level simulations to identify peptides that can recognize (1) the extracellular domain of EpCAM (a known cancer biomarker) and (2) the extracellular domain of tetraspanin CD81(a protein commonly expressed on the surface of EVs). The peptides designed for EpCAM and CD81 were labeled with a fluorescent dye and their binding to the target protein was evaluated using fluorescence ELISA. The results demonstrated that one of the computationally designed peptides EP-2.1 exhibited an affinity for the target EpCAM protein comparable to that of an antibody. Further testing involved single EV imaging to gauge the peptides affinity towards EVs. Designed peptides for both the target proteins showed similar affinity as antibodies to EVs.

cancer biology↗

bioRxiv2025

A gnotobiotic system reveals multifunctional effector roles in plant-fungal pathogen dynamics

Plants host diverse microbiota that influence physiological processes and can enhance resilience against invading pathogens that, in turn, evolved effector proteins to manipulate host microbiota in their favor. However, the complexity of microbial communities and their interactions complicates mechanistic research on processes governing microbiota assembly and function. Gnotobiotic systems are valuable tools to study plant microbiota by reducing complexity and enabling controlled microbiota reconstitution experiments. Despite their utility, no gnotobiotic systems have been established to investigate the role of antimicrobial effector proteins in the interactions between plants, their microbiota, and fungal pathogens. Here, we present a refined gnotobiotic system designed to study these interactions, establishing protocols for infections with the fungal pathogen Verticillium dahliae across multiple host plants under sterile conditions. We demonstrate that a synthetic microbial community (SynCom) derived from a culture collection generated for this study can be applied in this system where it interferes with fungal infections. Additionally, using our gnotobiotic system we reveal that specific antimicrobial effectors of V. dahliae, like Ave1L2, contribute to fungal virulence in a microbiota-dependent manner, whereas other antimicrobial effectors, such as Ave1, seem to possess functions beyond microbiota manipulation.

plant biology↗

bioRxiv2025

Intravenous lipid-siRNA conjugate mediates gene silencing at the blood-brain barrier and blood-CSF barrier

Barriers of the central nervous system (CNS), such as the blood-brain barrier (BBB) and blood-cerebrospinal fluid barrier (BCSFB), regulate the two-way exchange of material between the blood and CNS. These barriers pose a considerable challenge for efficacious delivery of intravenously administered therapies into the CNS, motivating exploration of their function and ways to modulate their properties. While the BBB and BCSFB can become dysfunctional in patients with chronic CNS diseases, few studies have focused on strategies for targeting these interfaces. Here, we showed that an intravenously administered albumin-binding lipid-siRNA conjugate was delivered to and silences genes within brain endothelial cells and choroid plexus epithelial cells, which comprise the BBB and BCSFB, respectively. A single intravenous dose of lipid-siRNA conjugate was delivered to [~]100% of brain endothelial cells and major choroid plexus cell types, without any substantial delivery into brain parenchymal tissue. Sustained gene silencing was achieved in both brain endothelial cells (over two weeks) and bulk choroid plexus tissues (up to one month). Moreover, single cell RNA sequencing demonstrated gene knockdown in capillaries, venous endothelial cells, and choroid plexus epithelial cells without silencing genes in parenchymal cell populations. Collectively, this work establishes an effective nonviral framework to mediate gene inhibition in the brain barriers. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=156 SRC="FIGDIR/small/642142v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@b00a52org.highwire.dtl.DTLVardef@175a363org.highwire.dtl.DTLVardef@39be75org.highwire.dtl.DTLVardef@1072093_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2025

Drug Repurposing through Meta-path Reconstruction using Relationship Embedding

De novo drug development are often costly, time-consuming and risky. Drug repurposing/repositioning, increasing usability of approved drugs, offers relatively high chance of success and efficiency based on the verified safety. Applying heterogeneous biological knowledge graph enabled compelling in silico drug repurposing, yet challenging to extract interaction between heterogeneous characteristics and utilizing multi-hop interactions. In this paper, I propose a PREDR model that predicts the drug-disease relationship by defining a drug-gene-disease meta-path from heterogeneous knowledge graphs and combining each heterogeneous relationship. The PREDR model reconstructs a meta-pathway based on relational information extracted by embedding each biological feature. The PREDR model outperformed compared to existing drug repurposing models in predicting drug-disease interaction, and demonstrated the effectiveness of meta-path reconstruction by showing higher performance than the result of learning and combining each heterogeneous relationships separately. The PREDR model can also explain the reaction mechanism of suggested drugs on the defined meta-pathway using heterogeneous interactions driven from reconstruction process. In predicting drug candidates for lymphoblastic leukemia disease conducted as a case study, the highest scored candidate is confirmed effectiveness of the disease in the literature, and predicted genes are verified to be targeted by both candidate and disease by various academic sources.

bioinformatics↗

bioRxiv2025

A hippocampal population code for rapid generalization

Generalizing from experience and applying prior knowledge to new situations is essential for intelligent behavior. Traditional models attribute this generalization to gradual statistical learning in the neocortex. However, such a slow process cannot account for animals rapid generalization from limited experience. Here, we demonstrate that the hippocampus supports rapid generalization in mice by generating disentangled memory representations, where different aspects of experience are encoded independently. This code enabled the transfer of prior knowledge to solve new tasks. We identify specific circuit mechanisms underlying this rapid generalization. We show that the seemingly random changes in individual neuronal activity over time and across environments result from structured circuit-level processes, governed by the dynamics of local inhibition and cross-regional cell assemblies, respectively. Our findings provide computational and mechanistic insights into how the geometric structure and underlying circuit organization of hippocampal population dynamics facilitate both memory discrimination and generalization, enabling efficient and flexible learning.

neuroscience↗

bioRxiv2025

Motion-corrected eye tracking (MoCET) improves gaze accuracy during visual fMRI experiments

Human eye movements are essential for understanding cognition, yet achieving high-precision eye tracking in fMRI remains challenging. Even slight head shifts from the initial calibration position can introduce drift in eye tracking data, leading to substantial gaze inaccuracies. To address this, we introduce Motion-Corrected Eye Tracking (MoCET), a novel approach that corrects drift using head motion parameters derived from the preprocessing of fMRI data. MoCET requires no additional hardware and can be applied retrospectively to existing datasets. We show that it outperforms traditional detrending methods with respect to accuracy of gaze estimation and offers higher spatial and temporal precision compared to MR-based eye tracking approaches. By overcoming a key limitation in integrating eye tracking with fMRI, MoCET facilitates investigations of naturalistic vision and cognition in fMRI research.

neuroscience↗

bioRxiv2025

Dissecting the molecular landscape of Parkinson's disease and Parkinson's disease dementia using highly efficient snRNA-seq (HIF-snRNA-seq)

This study presents a transcriptomic analysis of the cingulate cortex (CING) in Parkinsons disease (PD) and Parkinsons disease dementia (PDD) using a High-efficiency single-nucleus RNA sequencing (HiF-snRNA-seq) protocol optimized for post-mortem brain samples. RNA quality prediction, poly-A tailing, and dCas9-targeted depletion enabled analysis of 77 high-quality samples from 240 cases, yielding over 2 million nuclei classified into seven major cell types. Disease conditions revealed altered astrocyte and microglia proportions, implicating their roles in neuroinflammation. Differential expression analysis identified unique and shared genes across PD and PDD, linked to synaptic remodeling, stress responses, and inflammation. Stage-specific analysis uncovered tau-dependent early-stage genes and inflammation-associated late-stage genes. This study highlights the CINGs central role in PD and PDD pathophysiology, offering insights into disease mechanisms and identifying candidate genes and pathways for therapeutic and biomarker development.

genomics↗

bioRxiv2025

Human Milk Oligosaccharides Modulate Inflammatory Responses and Lipid Metabolism in a Human Intestinal Organoid Model

Human milk oligosaccharides (HMOs) are a major component of human breast milk and have significant protective effects on infant gut health. HMOs are also present in the amniotic fluid surrounding the developing fetus in the womb. Beginning at 10 weeks of gestational age, HMOs enter the fetal gut through the swallowing of amniotic fluid. The effects of this earliest exposure to HMOs on the gut epithelium, which pre-term infants partially miss, remains unknown. In this study, we investigate the effect of a blend of HMOs, including 2-fucosyllactose (2FL), 3-sialyllactose (3SL), and difucosyllactose (DFL), on intestinal epithelial cells, examining their role in steady-state conditions and during inflammation. By utilizing advanced intestinal epithelial organoid models derived from fetal and pediatric donors, we reveal developmental-stage-specific responses to this HMO blend, as well as its potential to mitigate inflammatory damage. These findings offer important insights into the role of HMOs in early-life nutrition and gut health, lending compelling evidence to support their inclusion in infant nutrition strategies.

cell biology↗