Biology subjects

Park, J.

Publications and source records attributed to Park, J..

At least 235 records · Page 13Linked to original sources

bioRxiv2024

An Autonomous Implantable Device for the Prevention of Death from Opioid Overdose

Opioid overdose accounts for nearly 75,000 deaths per year in the United States, representing a leading cause of mortality amongst the prime working age population (25-54 years). At overdose levels, opioid-induced respiratory depression becomes fatal without timely administration of the rescue drug naloxone. Currently, overdose survival relies entirely on bystander intervention, requiring a nearby person to discover and identify the overdosed individual, and have immediate access to naloxone to administer. Government efforts have focused on providing naloxone in abundance but do not address the equally critical component for overdose rescue: a willing and informed bystander. To address this unmet need, we developed the Naloximeter: a class of life-saving implantable devices that autonomously detect and treat overdose, with the ability to simultaneously contact first-responders. We present three Naloximeter platforms, for both fundamental research and clinical translation, all equipped with optical sensors, drug delivery mechanisms, and a supporting ecosystem of technology to counteract opioid-induced respiratory depression. In small and large animal studies, the Naloximeter rescues from otherwise fatal opioid overdose within minutes. This work introduces life-changing, clinically translatable technologies that broadly benefit a susceptible population recovering from opioid use disorder.

bioengineering↗

bioRxiv2024

AIVE: accurate predictions of SARS-CoV-2 infectivity from comprehensive analysis

An unprecedented amount of SARS-CoV-2 data has been accumulated compared with previous infectious diseases, enabling insights into its evolutionary process and more thorough analyses. This study investigates SARS-CoV-2 features as it evolved to evaluate its infectivity. We examined viral sequences and identified the polarity of amino acids in the Receptor Binding Motif (RBM) region. We detected an increased frequency of amino acid substitutions to lysine (K) and arginine (R) in Variants of Concern (VOCs). As the virus evolved to Omicron, commonly occurring mutations became fixed components of the new viral sequence. Furthermore, at specific positions of VOCs, only one type of amino acid substitution and a notable absence of mutations at D467 was detected. We found that the binding affinity of SARS-CoV-2 lineages to the ACE2 receptor was impacted by amino acid substitutions. Based on our discoveries, we developed APESS, an evaluation model evaluating infectivity from biochemical and mutational properties. In silico evaluation using real-world sequences and in vitro viral entry assays validated the accuracy of APESS and our discoveries. Using Machine Learning, we predicted mutations that had the potential to become more prominent. We created AIVE, a web-based system, accessible at https://ai-ve.org to provide infectivity measurements of mutations entered by users. Ultimately, we established a clear link between specific viral properties and increased infectivity, enhancing our understanding of SARS-CoV-2 and enabling more accurate predictions of the virus.

genomics↗

bioRxiv2024

Differential cell-ECM interaction of rhabdomyosarcoma subtypes regulated by PAX3-FOXO1

Rhabdomyosarcoma (RMS) is the most common childhood soft tissue sarcoma, with two subtypes: Fusion-positive RMS (FPRMS), which has the PAX3-FOXO1 fusion gene, and fusion-negative RMS (FNRMS). Despite their distinct characteristics, treatments mainly rely on conventional chemotherapies without considering these differences. This study highlights that FNRMS cells exhibit significantly heightened interaction with the extracellular matrix (ECM) compared to FPRMS cells. Using single-cell RNA sequencing of skeletal muscle tissues and RNA sequencing of RMS samples, we identified the upregulation of genes related to cell-ECM interaction and TGF{beta} signaling in FNRMS compared to FPRMS. We also confirmed enhanced cell-ECM interaction stimulated by TGF{beta} signaling in FNRMS cells, using confocal reflection microscopy to monitor dynamic cell-ECM interaction and a live-cell sensor to quantitatively assess TGF{beta} signaling activity. Additionally, we discovered that the PAX3-FOXO1 fusion gene, characteristic of FPRMS, stimulated nitric oxide synthesis, which suppresses TGF{beta} signaling and reduces cell-ECM interaction. These findings suggest that PAX3-FOXO1 determines the diminished cell-ECM interactions in FPRMS. Experimental data show higher sensitivity of FNRMS to cell-ECM interaction disruption and TGF{beta} inhibition. Furthermore, the diminished cell-ECM interaction in FPRMS, allowing cells to survive in the ectopic environment through circulation, may partly explain its higher metastatic potential compared to FNRMS.

cell biology↗

bioRxiv2024

Analysis of Unmapped RNA-seq Data from Cancer Spatial Transcriptome to Decipher Cancer Microbiome

Recent research increasingly emphasizes the importance of the microbiome in the development and progression of cancer. Thus, exploring the microbiome modulation in tumor microenvironment and understanding its composition and function are becoming important. The introduction of spatial transcriptomics has provided new insights into microbiome research, as it enables how microbiome affects tumor microenvironment. In this study, we analyzed the spatial distribution of microbial RNA observed through PathSeq and our extended method for unmapped RNA reads in oral squamous cell carcinoma, head and neck cancer, and colorectal cancer samples. Our novel method is designed to identify and classify microbial RNA, using a custom reference that includes species-specific microbial 16S rRNA sequences to enhance the accuracy of species-level microbiome analysis. The results of this study showed a potential for a deeper understanding of the microbial distribution and their functional roles within cancer tissues. These findings will reevaluate the role of the microbiome in cancer research, providing an insight for the development of microbiome-based therapies in the future.

bioinformatics↗

bioRxiv2024

Lipid-siRNA conjugate accesses a perivascular transport mechanism and achieves widespread and durable knockdown in the central nervous system

Short-interfering RNA (siRNA) has gained significant interest for treatment of neurological diseases by providing the capacity to achieve sustained inhibition of nearly any gene target. Yet, efficacious drug delivery throughout deep brain structures of the CNS remains a considerable hurdle for intrathecally administered therapeutics. We herein describe an albumin-binding lipid-siRNA conjugate that transports along meningeal and perivascular CSF pathways, leading to broad dispersion throughout the CNS parenchyma. We provide a detailed examination of the temporal kinetics of gene silencing, highlighting potent knockdown for up to five months from a single injection without detectable toxicity. Single-cell RNA sequencing further demonstrates gene silencing activity across diverse cell populations in the parenchyma and at brain borders, which may provide new avenues for neurological disease-modifying therapies.

bioengineering↗

bioRxiv2024

Molecular tension authenticates apoptotic cells being phagocytosed.

Profound cytoskeletal reorganization and plasma membrane deformation in phagocytes is indispensable for phagocytosis of massive apoptotic cells, but whether these dynamics accompany a mechanical signal modulating signaling during efferocytosis remains largely unexplored. Here, we report that tension between phosphatidylserine (PS) and PS receptors (PSR) generated at the phagocytic synapse serves as a signal to determine whether PS-exposing cells should be phagocytosed. Mechanistically, increased membrane tension of phagocytes via Rac1-dependent actin polymerization and membrane stiffness of apoptotic cells caused tension between PS and PSRs, leading to phosphoinositide 3-kinase recruitment to PSRs, which resulted in Rac1 inactivation and myosin II phosphorylation required for phagocytic cup closure. Our observations imply that tension between PS and PSRs acts as a mechanical fail-safe to prevent removal of all PS-exposing cells for the integrity of efferocytosis. One-Sentence SummaryTension between phosphatidylserine and its receptors acts as a final decision-maker determining phagocytosis of apoptotic cells.

cell biology↗

bioRxiv2024

Participatory science methods to monitor water quality and ground truth remote sensing of the Chesapeake Bay

Measurements by volunteer scientists using participatory science methods in combination with high resolution remote sensing can improve our ability to monitor water quality changes in highly vulnerable and economically valuable nearshore and estuarine habitats. In the Chesapeake Bay (USA), tidal tributaries are a focus of watershed and shoreline management efforts to improve water quality. The Chesapeake Water Watch program seeks to enhance the monitoring of tributaries by developing and testing methods for volunteer scientists to easily measure chlorophyll, turbidity, and colored dissolved organic matter (CDOM) to inform Bay stakeholders and improve algorithms for analogous remote sensing (RS) products. In the program, trained volunteers have measured surface turbidity using a smartphone app, HydroColor, calibrated with a photographers gray card. In vivo chlorophyll and CDOM fluorescence were assessed in surface samples with hand-held fluorometers (Aquafluor) located at sample processing "hubs" where volunteers drop-off samples for same day processing. In validation samples, HydroColor turbidity and Aquafluor in vivo chlorophyll and CDOM fluorescence were linearly related to standard analytical measures of turbidity, chlorophyll and CDOM, respectively, with R2 values ranging from 0.65 to 0.85. These methods are being used for both repeat sampling at fixed sites of interest and ad-hoc "blitzes" to synoptically sample tributaries all around the Bay in coordination with satellite overpasses. All data is accessible on a public database (serc.fieldscope.org) and can be a resource to monitor long-term trends in the tidal tributaries as well as detect and diagnose causes of events of concern such as algal blooms and storm-induced reductions in water clarity.

ecology↗

bioRxiv2024

Maintenance of haematopoietic stem cells by JAK inhibition and increased tyrosine-unphosphorylated STAT5

Normal and malignant hematopoietic stem cells (HSCs) are controlled by extracellular cues including cytokine signalling through the JAK/STAT pathway. Here, we show that STAT5-deficient HSCs exhibit an unusual phenotype: while reduced multi-lineage repopulation and reduced self-renewal are commonly associated with overproliferation and exhaustion, they are instead associated with reduced cell-cycle progression and increased differentiation in STAT5-deficient HSCs. Mechanistic studies show that unphosphorylated-STAT5 (uSTAT5) contributes to this phenotype by constraining HSC differentiation, promoting HSC maintenance and upregulating transcriptional programs associated with stemness. The JAK1/2 inhibitor ruxolitinib increases levels of uSTAT5, constrains differentiation and proliferation of murine HSCs, promotes their maintenance and upregulates transcriptional programs associated with stemness. Ruxolitinib also enhances clonogenicity of normal human HSPCs, CALR-mutant murine HSCs and HSPCs from patients with myelofibrosis. Our results therefore reveal a previously unrecognized role for uSTAT5 in controlling HSC function, highlight JAK inhibition as a strategy for enhancing HSC function and provide insights into the failure of JAK inhibitors to eradicate myeloproliferative neoplasms.

cell biology↗

bioRxiv2024

Dual-mode action of scalable, high-quality engineered stem cell-derived SIRP alpha extracellular vesicles for treating acute liver failure

Acute liver failure (ALF) is a critical inflammatory condition characterized by rapid hepatocyte death, impaired liver regeneration due to the delayed removal of necroptotic cells, and high mortality rates. This study introduces a novel dual-mode action therapeutic approach using extracellular vesicles expressing Signal Regulatory Protein Alpha (SIRP-EVs) derived from genetically engineered mesenchymal stem cells (MSCs). These SIRP-EVs are designed to concurrently resolve necroptosis and promote liver regeneration. Our studies identified CD47 and SIRP as promising therapeutic targets for ALF. We developed a scalable 3D bioreactor-based process that produces high-purity SIRP-EVs, which preserve MSC properties and achieve significant production levels. SIRP-EVs target both macrophages and necroptotic hepatocytes in ALF models, enhancing macrophage phagocytic activity against necroptotic cells via CD47 blockade and promoting liver regeneration by reprogramming macrophages with MSC-derived cargo. Comprehensive in vitro and in vivo studies demonstrate that SIRP-EVs decrease CD47+ necroptotic cells and promote liver regeneration in ALF models, leading to reduced liver damage markers and enhanced survival rates. These findings highlight the potential of SIRP-EVs as a dual-mode action therapeutic for ALF, offering promising prospects for their application in other inflammatory diseases. Moreover, these results pave the way for advancing engineered EV-based therapies toward clinical implementation.

bioengineering↗

bioRxiv2024

Younger adult brain utilizes interhemispheric strategy of recruiting ipsilateral dorsal premotor cortex for complex finger movement, but not aging brain

The ipsilateral sensorimotor cortices (dorsal premotor cortex [PMd], primary motor cortex [M1], primary somatosensory cortex [S1], and superior parietal cortex of Area 2) are often activated when the healthy younger and older adult brains perform complex finger movements. Prompted by clinical evidence that the ipsilateral PMd plays particularly important roles to complement the movements after stroke, we tested whether the ipsilateral PMd also plays particularly important (complementary) roles among the ipsilateral sensorimotor cortices when healthy younger adults perform a complex motor task by augmenting interhemispheric functional connectivity with the contralateral sensorimotor cortices. We also examined possible strategic difference when older adults with degraded interhemispheric inhibition perform the complex task when compared to younger adults with mature one. We addressed these questions by measuring brain activity with functional magnetic resonance imaging while healthy right-handed younger and older adults performed simple (button pressing with the right index finger) and complex (stick rotation requiring coordination between the right fingers) motor tasks. In younger group, the ipsilateral PMd, S1, Area 2 activated during the complex task, while the ipsilateral M1 remained deactivated as in the simple task, suggesting an existence of interregional difference. The ipsilateral PMd and S1/Area 2 more activated in the individuals with less dexterous performance. The anterior ipsilateral PMd enhanced interhemispheric functional coupling consistently with all of the contralateral sensorimotor cortices during the complex task. In contrast, in older group, all of the ipsilateral cortices including the M1 activated during the complex task, however, none of the cortices showed performance-related activity change. Increase in functional connectivity within the contralateral sensorimotor cortices rather than interhemispheric connectivity was observed during the complex task. The results suggest the importance and complementary role of the ipsilateral PMd for complex finger movement in the younger brains, and the strategic difference (interhemispheric vs. intrahemispheric) when the younger and aging brains perform the movement.

neuroscience↗

bioRxiv2024

Sex-focused analyses of M83 A53T hemizygous mouse model with recombinant human alpha-synuclein preformed fibril injection identifies female resilience to disease progression: A combined magnetic resonance imaging and behavioural study.

Alpha-synuclein (aSyn) pathology has been extensively studied in mouse models harbouring human mutations. In spite of the known sex differences in age of onset, prevalence and disease presentation in human synucleinopathies, the impact of sex on aSyn propagation has received very little attention. To address this need, we examined sex differences in whole brain signatures of neurodegeneration due to aSyn toxicity in the M83 mouse model using longitudinal magnetic resonance imaging (MRI; T1-weighted; 100 m3 isotropic voxel; acquired -7, 30, 90 and 120 days post-injection [dpi]; n[≥]8 mice/group/sex/time point). To initiate aSyn spreading, M83 mice were inoculated with recombinant human aSyn preformed fibrils (Hu-PFF) or phosphate buffered saline (PBS) injected in the right dorsal striatum. We observed more aggressive neurodegenerative profiles over time for male M83 Hu-PFF-injected mice when examining voxel-wise trajectories. However, at 90 dpi, we observed widespread patterns of neurodegeneration in the female Hu-PFF-injected mice. These differences were not accompanied with any differences in motor symptom onset between the male and female Hu-PFF-injected mice. However, male Hu-PFF-injected mice reached their humane endpoint sooner. These findings suggest that post-motor symptom onset, even though more accelerated disease trajectories were observed for male Hu-PFF-injected mice, neurodegeneration may appear sooner in female Hu-PFF-injected mice (prior to motor symptomatology). These findings suggest that sex-specific synucleinopathy phenotypes urgently need to be considered to improve our understanding of neuroprotective and neurodegenerative mechanisms.

neuroscience↗

bioRxiv2024

Phased ERK-responsiveness and developmental robustness regulate teleost skin morphogenesis

Elongation of the vertebrate embryonic axis necessitates rapid expansion of the epidermis to accommodate the growth of underlying tissues. Here, we generated a toolkit to visualize and quantify signaling in entire cell populations of periderm, the outermost layer of the epidermis, in live developing zebrafish. We find that oriented cell divisions facilitate growth of the early periderm during axial elongation rather than cell addition from the basal layer. Activity levels of ERK, a downstream effector of MAPK pathway, gauged by a live biosensor, predicts cell cycle entry, and optogenetic ERK activation controls proliferation dynamics. As development proceeds, rates of peridermal cell proliferation decrease, ERK activity becomes more pulsatile and functionally transitions to promote hypertrophic cell growth. Targeted genetic blockade of cell division generates animals with oversized periderm cells, yet, unexpectedly, development to adulthood is not impaired. Our findings reveal stage-dependent differential responsiveness to ERK signaling and marked developmental robustness in growing teleost skin.

developmental biology↗

bioRxiv2024

CELLama: Foundation Model for Single Cell and Spatial Transcriptomics by Cell Embedding Leveraging Language Model Abilities

Large-scale single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) have transformed biomedical research into a data-driven field, enabling the creation of comprehensive data atlases. These methodologies facilitate detailed understanding of biology and pathophysiology, aiding in the discovery of new therapeutic targets. However, the complexity and sheer volume of data from these technologies present analytical challenges, particularly in robust cell typing, integration and understanding complex spatial relationships of cells. To address these challenges, we developed CELLama (Cell Embedding Leverage Language Model Abilities), a framework that leverage language model to transform cell data into sentences that encapsulate gene expressions and metadata, enabling universal cellular data embedding for various analysis. CELLama, serving as a foundation model, supports flexible applications ranging from cell typing to the analysis of spatial contexts, independently of manual reference data selection or intricate dataset-specific analytical workflows. Our results demonstrate that CELLama has significant potential to transform cellular analysis in various contexts, from determining cell types across multi-tissue atlases and their interactions to unraveling intricate tissue dynamics.

bioinformatics↗

bioRxiv2024

Digital Profiling of Tumor Extracellular Vesicle-associated RNAs Directly from Unprocessed Blood Plasma

Tumor-derived extracellular vesicle (tEV)-associated RNAs hold promise as diagnostic biomarkers, but their clinical use is hindered by the rarity of tEVs among non-tumor EVs. Here, we present EV-CLIP, a highly sensitive droplet-based digital method for profiling EV RNA. EV-CLIP utilizes the fusion of EVs with charged liposomes (CLIPs) in a microfluidic chip. Optimized CLIP surface charge enables exceptional sensitivity and selectivity for EV-derived miRNAs and mRNAs. This approach streamlines detection with minimal plasma volume (20 {micro}L) and eliminates the need for prior EV isolation or RNA preparation, preventing loss of EVs or RNA. In testing with 83 patient samples, EV-CLIP detected EGFR L858R and T790M mutations with high AUC values of 1.0000 and 0.9784, respectively. Its success in serial monitoring during chemotherapy highlights its potential for precise quantification of rare EV subpopulations, facilitating the exploration of single EV RNA content and enhancing understanding of diverse EV populations in various disease states. SUMMARYEV-CLIP: A highly sensitive digital method for tumor-derived EV RNA detection using undiluted blood plasma samples, promising for precise tumor management.

bioengineering↗

bioRxiv2024

Noninvasive time-lapse 3D subcellular analysis of embryo development for machine learning-enabled prediction of blastocyst formation

Accurate embryo quality assessment is central to improving outcomes in in vitro fertilization (IVF), yet current practice relies mainly on subjective two-dimensional (2D) morphology. Here we present a label-free framework for quantitative three-dimensional (3D) embryo phenotyping using low-coherence holotomography (HT). Time-lapse HT enabled volumetric imaging of mouse embryos from the 2-cell stage to the blastocyst without affecting developmental competence, capturing subcellular features at high resolution. Quantitative analysis revealed that matured embryos exhibited higher blastomere counts, greater spatial variability, and tighter nuclear packing, whereas arrested embryos showed enlarged blastomeres, elevated cytoplasmic heterogeneity, and fewer, larger nuclei. Machine learning models trained on these features achieved robust prediction of blastocyst formation (AUC up to 0.958). Together, these findings demonstrate that HT provides objective and interpretable 3D biomarkers that could augment and transform embryo selection in IVF.

developmental biology↗

bioRxiv2024

Cholesterol Metabolite 27-Hydroxycholesterol Enhances the Secretion of Cancer Promoting Extracellular Vesicles by a Mitochondrial ROS-Induced Impairment of Lysosomal Function

Extracellular vesicles (EVs) serve as crucial mediators of cell-to-cell communication in normal physiology as well as in diseased states, and have been largely studied in regard to their role in cancer progression. However, the mechanisms by which their biogenesis and secretion are regulated by metabolic or endocrine factors remain unknown. Here, we delineate a mechanism by which EV secretion is regulated by a cholesterol metabolite, 27-Hydroxycholesterol (27HC), where treatment of myeloid immune cells (RAW 264.7 and J774A.1) with 27HC impairs lysosomal homeostasis, leading to shunting of multivesicular bodies (MVBs) away from lysosomal degradation, towards secretion as EVs. This impairment of lysosomal function is caused by mitochondrial dysfunction and subsequent increase in reactive oxygen species (ROS). Interestingly, cotreatment with a mitochondria-targeted antioxidant rescued the lysosomal impairment and attenuated the 27HC-mediated increase in EV secretion. Overall, our findings establish how a cholesterol metabolite regulates EV secretion and paves the way for the development of strategies to regulate cancer progression by controlling EV secretion.

cell biology↗

bioRxiv2024

Control of OPC proliferation and repopulation by the intellectual disability gene PAK1 under homeostatic and demyelinating conditions

Appropriate proliferation and repopulation of oligodendrocyte progenitor cells (OPCs) determine successful (re)myelination in homeostatic and demyelinating brains. Activating mutations in p21-activated kinase 1 (PAK1) cause intellectual disability, neurodevelopmental abnormality, and white matter anomaly in children. It remains unclear if and how PAK1 regulates oligodendroglial development. Here, we report that PAK1 controls proliferation and regeneration of OPCs. Unlike differentiating oligodendrocytes, OPCs display high PAK1 activity which maintains them in a proliferative state by modulating PDGFRa-mediated mitogenic signaling. PAK1-deficient or kinase-inhibited OPCs reduce their proliferation capacity and population expansion. Mice carrying OPC-specific PAK1 deletion or kinase inhibition are populated with fewer OPCs in the homeostatic and demyelinated CNS than control mice. Together, our findings suggest that kinase-activating PAK1 mutations stall OPCs in a progenitor state, impacting timely oligodendroglial differentiation in the CNS of affected children and that PAK1 is a potential molecular target for replenishing OPCs in demyelinating lesions.

neuroscience↗

bioRxiv2024

The molecular framework underlying the growth and defense tradeoff in Arabidopsis roots in response to danger signals

Elevated stress signaling often compromises plant growth by suppressing proliferative and formative divisions at the meristem. Plant Elicitor Peptide 1 (PEP1), an endogenous danger signal triggered by both biotic and abiotic stresses in Arabidopsis thaliana, suppresses proliferative divisions, alters xylem vessel organizations, and disrupts cell-to-cell symplastic connections in the root. To gain an insight into the dynamic molecular framework that modulates root development under elevated danger signals, we performed a time course RNA-sequencing analysis at the root meristem following PEP1 treatment. A series of data analyses revealed that STZ and its homologs are a potential nexus between the stress response and proliferative cell cycle regulation. We observed that STZ differentially controls the cell cycle, cell differentiation, and stress response genes at various tissue layers in the root meristem through various functional, phenotypic, and transcriptomic analyses. Our study further indicated that the expression level of STZ in response to stresses is critically important to enable the growth and defense tradeoff. The findings here provide valuable information about the dynamic gene expression changes upon perceiving danger signals at the root meristem and future engineering schemes to generate stress-resilient plants.

plant biology↗