Biology subjects

Ryu, T.

Publications and source records attributed to Ryu, T..

12 recordsLinked to original sources

bioRxiv2026

Human endogenous retrovirus envelope proteins alter extracellular vesicle cellular interactions and biodistribution

Extracellular vesicles (EVs) are versatile therapeutic candidates due to biological roles in intercellular communication and amenability to bioengineering. Compared with lipid nanoparticles (LNPs), native or surface-modified EVs may have favorable immunogenicity and biodistribution profiles. However, when administered intravenously (IV), EVs are rapidly cleared and accumulate mostly in the liver and spleen. With the goal of modifying EV biodistribution, we engineered EVs to display the human endogenous retrovirus (HERV) envelope glycoprotein Syncytin-1, an SLC1A5-binding fusogenic viral protein essential for syncytiotrophoblast formation in pregnancy. Here, we comprehensively characterize engineered Syncytin-1+ EVs, examine their interactions with cells in vitro, and assay biodistribution, immunogenicity, and pharmacokinetics ex vivo and in vivo in non-human primates. IV-administered Syncytin-1+ EVs are well tolerated, persist in the blood stream, and have altered organ biodistribution compared with unmodified EVs, suggesting therapeutic potential of Syncytin-1+ EVs at specific sites.

bioengineering↗

bioRxiv2026

Reactive Astrocytes Drive Extracellular Acidification to Mediate α-Synuclein Neurodegeneration

Astrocytes are increasingly recognized as key players in neurodegeneration1-3, yet the molecular mechanisms by which they drive disease remain elusive. Here, we uncover a fundamental pathway in which reactive astrocytes fuel neurodegeneration in -synucleinopathies--including Dementia with Lewy bodies and Parkinsons disease dementia--by acidifying the brains extracellular environment. We demonstrate that both human patient tissue and a gut-to-brain -synuclein mouse model exhibit accumulation of reactive astrocytes and extracellular acidosis. Mechanistically, we show that astrocytic lysosomal exocytosis releases acidic contents, driving a drop in pH that activates neuronal acid-sensing ion channel 1a (ASIC1a), resulting in neuronal loss and behavioral decline. Blocking this pathway--either by inhibiting astrocytic lysosomal exocytosis or genetically or pharmacologically targeting neuronal ASIC1a--mitigates pathology and rescues neurodegenerative phenotypes in vivo. These findings provide a conceptual advance by establishing a mechanistic link between glial inflammation, acid-base homeostasis, and neuronal vulnerability, and suggest that targeting astrocyte-driven acidification or ASIC1a signaling could offer new avenues for disease modification in -synucleinopathies.

neuroscience↗

bioRxiv2025

Uncovering Design and Assembly Rules for mRNA-DNA Origami

mRNA-DNA hybrid origami offers a powerful route to combine the structural programmability of DNA origami with the biological functionality of messenger RNA, but generalizable design and assembly rules for these hybrids remain poorly defined. Here we systematically investigate the design principles and synthesis conditions that govern high-yield formation of mRNA-DNA hybrid nanostructures. Using mature mRNAs encoding firefly luciferase, EGFP, and mCherry as scaffolds, we construct a series of five hybrid compact origamis with diverse sizes, shapes, crossover strategies, and packing densities. We identify key parameters that control folding fidelity, including asymmetric A-form crossovers, monovalent-cation concentrations, and moderate-temperature annealing protocols, which together mitigate RNA instability, reduce kinetic traps, and accommodate RNA-DNA helical geometry. Atomic force microscopy reveals monodisperse, well-folded structures consistent with design expectations across most architectures and confirms that optimized conditions produce nanoscale precision comparable to DNA origami. Our findings establish generalizable design rules and a standard synthesis protocol for mRNA-DNA hybrid origami, providing a framework for their use in gene delivery and other RNA-based nanotechnologies.

bioengineering↗

bioRxiv2025

Extracellular Vesicles from Multiple Sclerosis White Matter Exhibit Synaptic, Mitochondrial, Complement, and Aging-related Pathway Dysregulation

Extracellular vesicles (EVs) are increasingly recognized as mediators of central nervous system (CNS) function and pathologies, including multiple sclerosis (MS). While plasma-derived EVs have been explored as biomarkers in MS, little is known about EVs in CNS tissue. Here, we characterize EVs from postmortem white matter (WM) of MS and control brains. EVs were separated by differential centrifugation followed by size exclusion chromatography and characterized using nanoflow cytometry, single-particle reflectance imaging sensing (SP-IRIS), and transmission electron microscopy. EV size, yield, and morphology did not differ significantly between MS and control samples. Proteomic analyses revealed downregulation of synaptic and mitochondrial proteins and upregulation of complement and inflammatory proteins and pathways in MS WM EVs. This suggests that EVs reflect ongoing synaptic pathology, metabolic dysfunction, and CNS-compartmentalized inflammation and that they may actively contribute to these pathological processes. Deconvolution analyses suggests a shift in EV cellular origin, with an increased astrocytic and decreased neuronal EV contributions in MS. Several proteomic changes we observed in CNS-derived EVs have also been reported in circulating EVs of people with MS, establishing this CNS tissue EV study as a valuable resource for identifying biomarker candidates for brain-derived plasma EV studies. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=136 SRC="FIGDIR/small/657509v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@1f88da5org.highwire.dtl.DTLVardef@11b7ee9org.highwire.dtl.DTLVardef@291d9forg.highwire.dtl.DTLVardef@157cb73_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2023

'Off-pore' nucleoporins relocalize heterochromatic breaks through phase separation

Phase separation forms membraneless compartments in the nuclei, including by establishing heterochromatin "domains" and repair foci. Pericentromeric heterochromatin mostly comprises repeated sequences prone to aberrant recombination, and "safe" homologous recombination (HR) repair of these sequences requires the movement of repair sites to the nuclear periphery before Rad51 recruitment and strand invasion. How this mobilization initiates is unknown, and the contribution of phase separation to these dynamics is unclear. Here, we show that Nup98 nucleoporin is recruited to heterochromatic repair sites before relocalization through Sec13 or Nup88 nucleoporins, and downstream from the Smc5/6 complex and SUMOylation. Remarkably, the phase separation properties of Nup98 are required and sufficient to mobilize repair sites and exclude Rad51, thus preventing aberrant recombination while promoting HR repair. Disrupting this pathway results in heterochromatin repair defects and widespread chromosome rearrangements, revealing a novel "off-pore" role for nucleoporins and phase separation in nuclear dynamics and genome integrity in a multicellular eukaryote. HighlightsO_LINup88 and Sec13 recruit Nup98 to heterochromatic DSBs downstream from Smc5/6 C_LIO_LINup88, Sec13 and Nup98 promote repair focus mobilization in heterochromatin off-pore C_LIO_LINup98 excludes Rad51 from repair sites inside the heterochromatin domain C_LIO_LIPhase separation by Nup98 is required and sufficient for relocalization and Rad51 exclusion C_LI

cell biology↗

bioRxiv2023

Development of an in situ cell-type specific proteome analysis method using antibody-mediated biotinylation

Since proteins are essential molecules exerting cellular functions, decoding proteome changes is the key to understanding the normal physiology and pathogenesis mechanism of various diseases. However, conventional proteomic studies are often conducted on tissue lumps, in which multiple cell types are entangled, presenting challenges in interpreting the biological dynamics among diverse cell types. While recent cell-specific proteome analysis techniques, like BONCAT, TurboID, and APEX, have emerged, their necessity for genetic modifications limits their usage. The alternative, laser capture microdissection (LCM), although it does not require genetic alterations, is labor-intensive, time-consuming, and requires specialized expertise, making it less suitable for large-scale studies. In this study, we develop the method for in situ cell-type specific proteome analysis using antibody-mediated biotinylation (iCAB), in which we combined immunohistochemistry (IHC) with the biotin-tyramide signal amplification approach. Poly-horseradish peroxidase (HRP) conjugated to the secondary antibody will be localized at a target cell type via a primary antibody specific to the target cell type and biotin-tyramide activated by HRP will biotinylate the nearby proteins. Therefore, the iCAB method can be applied to any tissues that can be used for IHC. As a proof-of-concept, we employed iCAB for mouse brain tissue enriching proteins for neuronal cell bodies, astrocytes, and microglia, followed by identifying the enriched proteins using 16-plex TMT-based proteomics. In total, we identified [~]8,400 and [~]6,200 proteins from enriched and non-enriched samples. Most proteins from the enriched samples showed differential expressions when we compared different cell type data, while there were no differentially expressed proteins from non-enriched samples. The cell type enrichment analysis with the increased proteins in respective cell types using Azimuth showed that neuronal cell bodies, astrocytes, and microglia data exhibited Glutamatergic Neuron, Astrocyte and Microglia/Perivascular Macrophage as the representative cell types, respectively. The proteome data of the enriched proteins showed similar subcellular distribution as non-enriched proteins, indicating that the iCAB-proteome is not biased toward any subcellular compartment. To our best knowledge, this study represents the first implementation of a cell-type-specific proteome analysis method using an antibody-mediated biotinylation approach. This development paves the way for the routine and widespread use of cell-type-specific proteome analysis. Ultimately, this could accelerate our understanding of biological and pathological phenomena.

systems biology↗

bioRxiv2022

The chromosome-scale genome assembly of the yellowtail clownfish Amphiprion clarkii provides insights into melanic pigmentation of anemonefish

Anemonefish are an emerging group of model organisms for studying genetic, ecological, evolutionary, and developmental traits of coral reef fish. The yellowtail clownfish Amphiprion clarkii possesses species-specific characteristics such as inter-species co-habitation, high intra-species color variation, no anemone specificity, and a broad geographic distribution, that can increase our understanding of anemonefish evolutionary history, behavioral strategies, fish-anemone symbiosis, and color pattern evolution. Despite its position as an emerging model species, the genome of A. clarkii is yet to be published. Using PacBio long-read sequencing and Hi-C chromatin capture technology, we generated a high-quality chromosome-scale genome assembly initially comprised of 1,840 contigs with an N50 of 1,203,211 bp. These contigs were successfully anchored into 24 chromosomes of 843,582,782 bp and annotated with 25,050 protein-coding genes encompassing 97.0 % of conserved actinopterygian genes, making the quality and completeness of this genome the highest amongst all published anemonefish genomes to date. Transcriptomic analysis identified tissue-specific gene expression patterns, with the brain and optic lobe having the largest number of expressed genes. Further analyses revealed higher copy numbers of erbb3b (a gene involved in melanophore development) in A. clarkii compared to other anemonefish, thus suggesting a possible link between erbb3b and the natural melanism polymorphism observed in A. clarkii. The publication of this high-quality genome, along with A. clarkiis many unique traits, position this species as an ideal model organism for addressing scientific questions across a range of disciplines.

genomics↗

bioRxiv2022

A chromosome-scale genome assembly of the false clownfish, Amphiprion ocellaris

BackgroundThe false clownfish Amphiprion ocellaris is a popular fish species and an emerging model organism for studying the ecology, evolution, adaptation, and developmental biology of reef fishes. Despite this, high-quality genomic resources for this species are scarce, hindering advanced genomic analyses. Leveraging the power of PacBio long-read sequencing and Hi-C chromosome conformation capture techniques, we constructed a high-quality chromosome-scale genome assembly for the clownfish A. ocellaris. ResultsThe initial genome assembly comprised of 1,551 contigs of 861.42 Mb, with an N50 of 863.85 kb. Hi-C scaffolding of the genome resulted in 24 chromosomes containing 856.61 Mb. The genome was annotated with 26,797 protein-coding genes and had 96.62 % completeness of conserved actinopterygian genes, making this genome the most complete and high quality among published anemonefish genomes. Transcriptomic analysis identified tissue-specific gene expression patterns, with the brain and optic lobe having the largest number of expressed genes. Further, comparative genomic analysis revealed 91 genome elements conserved only in A. ocellaris and its sister species Amphiprion percula, and not in other anemonefish species. These elements are close to genes that are involved in various nervous system functions and exhibited distinct expression patterns in brain tissue, potentially highlighting the genetic toolkits involved in lineage-specific divergence and behaviors of the clownfish branch. ConclusionsOverall, our study provides the highest quality A. ocellaris genome assembly and annotation to date, whilst also providing a valuable resource for understanding the ecology and evolution of reef fishes.

genomics↗

bioRxiv2020

DNA micro-disk for the management of DNA-based data storage with index and write-once-read-many (WORM) memory features

DNA-based data storage has attracted attention because of its higher physical density of the data and longer retention time than those of conventional digital data storage1-7. However, previous DNA-based data storage lacked index features and the data quality of storage after a single access is not preserved, obstructing its industrial use. Here, we propose DNA micro-disks, quick response (QR)-coded micro-sized disks that harbour data-encoded DNA molecules for the efficient management of DNA-based data storage. We demonstrate the two major features that previous DNA-based data storage studies could not achieve. One feature is accessing data items efficiently by indexing the data-encoded DNA library. Another is achieving write-once-read-many (WORM) memory through the immobilization of DNA molecules on the disk and their enrichment through in situ DNA production. Through these features, the reliability of DNA-based data storage was increased by allowing multiple accession of data-encoded DNA without data loss.

bioengineering↗

bioRxiv2018

The draft genome of an octocoral, Dendronephthya gigantea

BackgroundCoral reefs composed of stony corals are threatened by global marine environmental changes. However, soft coral communities composed of octocorallian species, appear more resilient. The genomes of several species of cnidarians have been published, including stony corals, sea anemones, and hydra, but as of yet no octocoral species. To fill this phylogenetic gap within the cnidarian, we sequenced the octocoral, Dendronephthya gigantea, a non-symbiotic soft coral, commonly known as the carnation coral.\n\nFindingsThe D. gigantea genome size is approximately 276 Mb. A high-quality genome assembly was constructed using 29.85Gb (108x coverage) of PacBio long reads and 35.54Gb (128x coverage) of Illumina short paired-end reads resulting in the largest N50 value reported among cnidarian of 1.4 Mb. About 12 % of the genome consisted of repetitive elements. We found 28,879 protein-coding genes. This gene set contained about 94% metazoan single-copy orthologs, indicating the gene models were predicted with high quality compared to other cnidarians. Based on molecular phylogenetic analysis, octocoral and hexacoral divergence occurred approximately 544 million years ago. Moreover, there is a clear difference in Hox gene composition: unlike in hexacorals, Antp superclass member Evx gene was absent in D. gigantea.\n\nConclusionsWe present the first genome assembly of a non-symbiotic octocoral, D. gigantea to aid in the comparative genomic analysis of cnidarians, including comparisons of stony and soft corals and symbiotic and non-symbiotic corals. In addition, the genome of this species may provide clues about differential genetic coping mechanisms between soft and stony coral regarding the global warming.

genomics↗

bioRxiv2018

High-throughput retrieval of physical DNA for NGS-identifiable clones in phage display library

In antibody discovery, in-depth analysis of an antibody library and high-throughput retrieval of clones in the library are crucial to identifying and exploiting rare clones with different properties. However, existing methods have several technical limitations such as low process throughput from laborious cloning process and waste of the phenotypic screening capacity from unnecessary repetitive tests on the dominant clones. To overcome the limitations, we developed a new high-throughput platform for the identification and retrieval of clones in the library, TrueRepertoire. TrueRepertoire provides highly accurate sequences of the clones with linkage information between heavy and light chains of the antibody fragment. Additionally, the physical DNA of clones can be retrieved in high throughput based on the sequence information. We validated the high accuracy of the sequences and demonstrated that there is no platform-specific bias. Moreover, the applicability of TrueRepertoire was demonstrated by a phage-displayed single-chain variable fragment (scFv) library targeting human hepatocyte growth factor (hHGF) protein.

bioengineering↗

bioRxiv2018

Addition of Degenerate Bases to DNA-based Data Storage for Increased Information Capacity

Introductory paragraphDNA-based data storage has emerged as a promising method to satisfy the exponentially increasing demand for information storage. However, practical implementation of DNA-based data storage remains a challenge because of the high cost of DNA per unit data. Here, we propose the use of eleven degenerate bases as encoding characters in addition to A, C, G, and T, which increases the information capacity (the amount of data that can be stored per length of DNA sequence designed) and reduce the cost of DNA per unit data. Using the proposed method, we experimentally achieved an information capacity of 3.37 bits/character, which is more than twice when compared to the highest information capacity previously achieved. Finally, the platform was projected to reduce the cost of DNA-based data storage by 50%.

synthetic biology↗