Biology subjects

Okada, R.

Publications and source records attributed to Okada, R..

16 recordsLinked to original sources

bioRxiv2026

NLGN3-tagging system for Evaluating Membrane Localization Applied to Drug Screening

Aberrant membrane localization of proteins often results in functional impairment, contributing to the development of pathological conditions. Neuroligin-3 (NLGN3) is a rare but recurrent genetic risk factor for autism spectrum disorder (ASD). Comparing surface localization across NLGN3 variants requires that surface signal be referenced to expression level in the same cell. Using NLGN3 as a model, we developed I-CLiQ, a live-cell method in which the target coding sequence is introduced at a single site of a fixed vector backbone and DsRed is co-encoded as an internal expression reference, based on a 2A peptide of Perina nuda virus modified to abolish ribosomal skipping. Combining I-CLiQ with AlphaFold/AlphaMissense analysis, we evaluated ASD-associated NLGN3 variants. Structural modeling predicted steric clashes for p.R451C, p.P514S, and p.R597W. I-CLiQ-based flow cytometry confirmed that these variants significantly decrease surface expression. Furthermore, as a proof-of-concept application, we used I-CLiQ to evaluate two compounds, 4-phenylbutyrate (4-PBA) and 3-amino-1-propanesulfonic acid (3-APS); 4-PBA partially restored the surface expression of p.R451C and p.R597W. These findings establish I-CLiQ as a quantitative tool for analyzing membrane trafficking defects and demonstrate its applicability to compound screening for variants associated with conformational diseases.

cell biology↗

bioRxiv2026

Regucalcin-containing extracellular vesicles suppress M2 macrophage polarization and attenuate tumor progression in vivo

Regucalcin (RGN) plays diverse roles in cell biology, highlighting its importance in both physiological and pathological conditions. Prostate cancer patients with higher RGN expression exhibited significantly longer disease-free survival. Although RGN is a cell signaling suppressor, the molecular mechanisms underlying tumor suppression by RGN in the tumor microenvironment through cell-cell communication remain unclear. PC3 prostate cancer cell lines stably expressing RGN or a control vector were generated for this study. Extracellular vesicles (EVs) were isolated from these cell lines using differential ultracentrifugation. The murine macrophage cell line J7441 was treated with isolated EVs, and effects on M2 polarization were evaluated using qRT-PCR and western blot analysis. To assess the potential anti-tumor effects of EVs, PC3 parental cells were subcutaneously implanted at two sites per mouse, followed by intratumoral injection of the respective EVs. Tumor volume was monitored. Harvested fresh frozen tumor tissues underwent immunofluorescence staining for CD206, an M2 macrophage marker. RGN was detected in EVs from RGN-expressing cells, and treatment with these RGN-containing EVs was associated with reduced tumor growth and reduced M2 macrophage polarization in vitro and in vivo. Furthermore, recombinant RGN protein reduced the levels of p-AKT1 and p-ERK1/2. Moreover, the suppression of M2 macrophage polarization by RGN-containing EVs was accompanied by decreased p-AKT1 and p-ERK1/2 in vitro. This study describes an EV-associated mechanism that may contribute to the regulation of macrophage polarization and indicates that RGN-containing EVs merit further evaluation as a candidate approach for cancer treatment. Causal validation, such as macrophage depletion or CD206 knockdown, and evaluation in additional models remain to be addressed in future studies.

cancer biology↗

bioRxiv2025

Early pathogenesis of spinal and bulbar muscular atrophy uncovered by human iPSC-derived motor neurons highlights pathogenic neuropeptides as therapeutic targets

Spinal and bulbar muscular atrophy (SBMA) is a neuromuscular disorder caused by the expansion of the polyglutamine tract in the androgen receptor (AR). Motor neurons (MNs) derived from patient-specific induced pluripotent stem cells (iPSCs) robustl y recapitulated early SBMA phenotypes driven by endogenous mutant AR in the absence of testosterone (dihydrotestosterone) and detectable mutant AR aggregation. Notably, endoplasmic reticulum stress markedly exacerbated SBMA pathology. Cross-species integrative analyses of patient-derived neurons and spinal cords of transgenic mouse models revealed high expression of multiple disease-associated neuropeptides, including urotensin II (UTS2), in patient spinal MNs that was correlated with disease onset and progression in iPSC-derived MNs. Downstream signaling analyses of these neuropeptides revealed convergent molecular pathways whose pharmacological inhibition rescued cellular phenotypes. Together, these results establish a human disease model harboring endogenous mutant AR that closely reproduces early SBMA pathology and provides molecular leads for elucidating disease mechanisms and biomarkers and developing therapeutic targets.

neuroscience↗

bioRxiv2025

MoChia1 is a family 18 glycoside hydrolase from the rice blast fungus, Magnaporthe oryzae, that releases reducing-end GlcNAc from chitin oligosaccharides

MoChia1, a family 18 glycoside hydrolase from the rice blast fungus Magnaporthe oryzae, was identified as an enzyme that binds chitin oligosaccharide elicitor to suppress the chitin-induced rice immune response. It hydrolyzed chitin oligosaccharides with a degree of polymerization of at least 3 [(GlcNAc)n (n[≥]3)] in an exo-splitting manner with anomeric retention. HPLC analysis of (GlcNAc)n cleavage by MoChia1 revealed that it specifically recognizes the {beta}-anomer of the substrate at the + 1 subsite and cleaves the terminal glycosidic linkage at the reducing end. It also hydrolyzed the partially deacetylated chitotrisaccharide GlcN-(GlcNAc)2 to GlcN-GlcNAc and GlcNAc, but not (GlcN)2-GlcNAc, indicating the requirement of the N-acetyl group at the -1 subsite for the hydrolytic reaction. MoChia1 released p-nitrophenol from pNP-(GlcNAc)2, p-nitrophenyl di-N-acetyl-{beta}-chitotrioside. Furthermore, it hydrolyzed the chitotriose derivatives with a modified GlcNAc residue on the reducing end, (GlcNAc)2-G, 4-O-{beta}-di-N-acetylchitobiosyl-2-acetamido-2-deoxy-2,3-anhydro-glucopyranose and (GlcNAc)2-L, 4-O-{beta}-di-N-acetylchitobiosyl-2-acetamido-2-deoxy-2,3-anhydro-glucono-{delta}-lactone, to (GlcNAc)2 and the modified GlcNAc, respectively. However, it did not hydrolyze 4-O-{beta}-di-N-acetylchitobiosyl moranoline [(GlcNAc)2-M], reduced chitotriose (chitotriitol), and -(GlcNAc)2 fluoride [(-(GlcNAc)2-F]. MoChia1 did not bind to chitin and barely hydrolyzed the polymeric substrate, glycol chitin. Taken together, we concluded that MoChia1 is a GH18 reducing end GlcNAc-releasing exo-oligochitinase with the {beta}-anomer selectivity. Allosamidin, a potent inhibitor of GH18 chitinases, was found to bind to MoChia1 and inhibit its hydrolytic activity with an IC50 of 54.4 {+/-} 6.91 M, indicating that allosamidin may be a potential candidate for a pesticide to prevent rice blast infection by inhibiting the chitinase activity of MoChia1.

biochemistry↗

bioRxiv2025

ibSLS: A Biobank for Democratizing Access to Multi-Omics Data and Biospecimens from Spaceflight Research

During spaceflight, astronauts are exposed to extreme conditions such as microgravity, cosmic radiation, and confinement, which can cause a wide range of health problems. To elucidate the molecular mechanisms underlying these issues and to develop intervention strategies for maintaining physiological homeostasis during space missions, space life science research using mouse models is actively conducted on the International Space Station (ISS). However, because of the high cost and technical complexity of spaceflight experiments, it is critical to maximize the scientific value of each mission by ensuring broad accessibility to both data and biospecimens. To this end, we developed the integrated biobank for Space Life Sciences (ibSLS; https://ibsls.megabank.tohoku.ac.jp), a data-visualization and sample-sharing platform that provides access to transcriptomic and metabolomic datasets generated from JAXAs Mouse Habitat Unit (MHU) missions. The platform features a user-friendly interface, tools for cross-mission analysis, and integration with human multi-omics databases, enabling cross-species comparisons. In addition, ibSLS facilitates biospecimen requests to support downstream research. By promoting open access to spaceflight-derived data and biological resources, ibSLS encourages the participation of researchers from diverse fields in space life science. We believe that ibSLS will make a valuable contribution to both biomedical research on spaceflight-related health issues and the study of diseases on Earth.

bioinformatics↗

bioRxiv2025

Storage Protein-Mediated Translation Control Links Juvenile Diet to Longevity in Drosophila

Dietary restriction (DR), whether applied during adulthood or juvenile stages, extends lifespan across diverse species. However, the mechanisms by which early-life dietary interventions influence adult physiology and longevity remain poorly understood. Here, using Drosophila as a model, we demonstrate that protein restriction during the larval stage (early-life protein restriction, ePR) promotes adult lifespan by reducing storage protein levels. Stable isotope tracing reveals that dietary amino acids obtained in the larval stage are retained into adulthood, especially incorporated into ribosomal proteins. This is mediated by larval serum protein 2 (Lsp2), a major storage protein, whose expression is durably downregulated by ePR. Both dietary (ePR) and genetic (Lsp2-RNAi) reduction of the protein storage lead to decreased ribosomal protein levels and translation activity in early adulthood. Notably, these storage proteins are enriched in aromatic amino acids such as tyrosine, and larval tyrosine restriction alone is sufficient to suppress translation and promote longevity. These findings show that storage proteins mediate the effect of larval nutrition on adult longevity via controlling translation. Our study uncovers a previously unrecognised mechanism of nutritional memory that links early-life diet to life-long organismal health.

physiology↗

bioRxiv2024

Identification of DLK1, a Notch ligand, as an immunotherapeutic target and regulator of tumor cell plasticity and chemoresistance in adrenocortical carcinoma

Immunotherapeutic targeting of cell surface proteins is an increasingly effective cancer therapy. However, given the limited number of current targets, the identification of new surface proteins, particularly those with biological importance, is critical. Here, we uncover delta-like non-canonical Notch ligand 1 (DLK1) as a cell surface protein with limited normal tissue expression and high expression in multiple refractory adult metastatic cancers including small cell lung cancer (SCLC) and adrenocortical carcinoma (ACC), a rare cancer with few effective therapies. In ACC, ADCT-701, a DLK1 targeting antibody-drug conjugate (ADC), shows potent in vitro activity among established cell lines and a new cohort of patient-derived organoids as well as robust in vivo anti-tumor responses in cell line-derived and patient-derived xenografts. However, ADCT-701 efficacy is overall limited in ACC due to high expression and activity of the drug efflux protein ABCB1 (MDR1, P-glycoprotein). In contrast, ADCT-701 is extremely potent and induces complete responses in DLK1+ ACC and SCLC in vivo models with low or no ABCB1 expression. Genetic deletion of DLK1 in ACC dramatically downregulates ABCB1 and increases ADC payload and chemotherapy sensitivity through NOTCH1-mediated adrenocortical de-differentiation. Single cell RNA-seq of ACC metastatic tumors reveals significantly decreased adrenocortical differentiation in DLK low or negative cells compared to DLK1 positive cells. This works identifies DLK1 as a novel immunotherapeutic target that regulates tumor cell plasticity and chemoresistance in ACC. Our data support targeting DLK1 with an ADC in ACC and neuroendocrine neoplasms in an active first-in-human phase I clinical trial (NCT06041516).

cancer biology↗

bioRxiv2024

Identification of a novel mycovirus belonging to the ''flexivirus''-related family with icosahedral virion

The order Tymovirales currently comprises five viral families with positive-sense RNA ((+)RNA) genomes that infect plants, fungi, and insects. Virion morphologies within the order Tymovirales differ between families, with icosahedral virions in the Tymoviridae and filamentous virions in the other "flexi"viridae families. Despite their different morphologies, these viruses are placed in the same order based on phylogenetic analyses of replicase-associated polyproteins. However, one of the families in the Tymovirales, Deltaflexiviridae, is considered to be capsidless because there have been no published reports of virion isolation. Here we report that a new "flexivirus"-related (+)RNA virus, prospectively named Fusarium oxysporum icosahedral virus 1 (FoIV1), is icosahedral, and that most deltaflexiviruses may have icosahedral virions. Phylogenetic analyses based on replicase-associated polyproteins indicated that FoIV1 forms a distinct group in the Tymovirales with some viruses originally assigned to the Deltaflexiviridae. Electron microscopy, protein analysis, and protein structure predictions indicate that FoIV1 ORF4 encodes a single jelly-roll (SJR)-like coat protein (CP) that constitutes the icosahedral virions. Results of clustering analyses based on amino acid sequences and predicted CP structures suggested that most of the deltaflexiviruses have icosahedral virions composed of SJR-like CPs as in FoIV1, rather than having filamentous virions or capsidless. These results challenge the conventional understanding of viruses in the order Tymovirales, with important implications for revising its taxonomic framework and providing insights into the evolutionary relationships within this diverse and broad host range group of (+)RNA viruses.

microbiology↗

bioRxiv2024

Dietary zinc restriction mimics protein restriction and extends lifespan in Drosophila

Dietary restriction extends lifespan in model organisms, mainly through dietary amino acids. Compared to macronutrients, the effect of dietary micronutrients on organismal lifespan has not been intensively investigated. Here, using a synthetic diet, we test whether restriction of each micronutrient, including vitamins and minerals, affects lifespan and fecundity in adult Drosophila. While restriction of many of these micronutrients have either negative or no impact on lifespan, zinc (Zn) restriction alone can increase it. Dietary Zn restriction (ZnR) decreases fecundity, increases starvation resistance, and promotes preference for feeding amino acids, in adult females, phenocopying dietary amino acid restriction. Our study demonstrates that dietary intake of trace elements has profound impacts on physiology and lifespan, and that limiting dietary zinc may be a strategy to improve the healthspan of animals.

physiology↗

bioRxiv2023

Dual-specificity phosphatases 13 and 27 as key switches in muscle stem cell transition from proliferation to differentiation

Muscle regeneration depends on muscle stem cell (MuSC) activity. Myogenic regulatory factors, including myoblast determination protein 1 (MyoD), regulate the fate transition of MuSCs. However, the direct target of MYOD in the process is not completely clear. Using previously established MyoD knock-in (MyoD-KI) mice, we revealed that MyoD targets dual-specificity phosphatase (Dusp) 13 and Dusp27. In Dusp13:Dusp27 double knock-out (DKO) mice, the ability for muscle regeneration after injury was reduced. Moreover, single-cell RNA sequencing of MyoD-high expressing MuSCs from MyoD-KI mice revealed that Dusp13 and Dusp27 are expressed only in specific populations within MyoD-high MuSCs, which also express Myogenin. Overexpressing Dusp13 in MuSCs causes premature muscle differentiation. Thus, we propose a model where DUSP13 and DUSP27 contribute to the fate transition of MuSCs from proliferation to differentiation during myogenesis. Significance StatementMYOD protein is not expressed in quiescent muscle stem cells but accumulates rapidly following muscle injury, leading to the proliferation of myogenic progenitors for differentiation. However, the direct targets of MYOD, aside from myogenin, which play roles in myogenic differentiation remain incompletely understood. Using previously established MyoD knock-in mice and single-cell RNA sequencing, we discovered that Dusp13 and Dusp27 are potential target genes of MYOD that promote myogenesis during muscle regeneration in adult mice.

cell biology↗

bioRxiv2023

Microfluidic device for simple diagnosis of plant growth condition by detecting miRNAs from filtered plant extracts

Plants are exposed to a variety of environmental stress and starvation of inorganic phosphorus can be a major constraint in crop production. In plants, in response to phosphate deficiency in soil, miR399, a type of microRNA (miRNA), is upregulated. By detecting miR399, the early diagnosis of phosphorus deficiency stress in plants can be accomplished. However, general miRNA detection methods require complicated experimental manipulations. Therefore, simple and rapid miRNA detection methods are required for early plant nutritional diagnosis. For the simple detection of miR399, microfluidic technology is suitable for point-of-care applications because of its ability to detect target molecules in small amounts in a short time and with simple manipulation. In this study, we developed a microfluidic device to detect miRNAs from filtered plant extracts for the easy diagnosis of plant growth conditions. To fabricate the microfluidic device, verification of the amine-terminated glass as the basis of the device and the DNA probe immobilization method on the glass was conducted. In this device, the target miRNAs were detected by fluorescence of sandwich hybridization in a microfluidic channel. For plant stress diagnostics using a microfluidic device, we developed a protocol for miRNA detection by validating the sample preparation buffer, filtering, and signal amplification. Using this system, endogenous sly-miR399 in tomatoes, which is expressed in response to phosphorus deficiency, was detected before the appearance of stress symptoms. This early diagnosis system of plant growth conditions has a potential to improve food production and sustainability through cultivation management.

plant biology↗

bioRxiv2023

Early-adult methionine restriction reduces methionine sulfoxide and extends lifespan in Drosophila

Methionine restriction (MetR) extends lifespan in various organisms, but its mechanistic understanding remains incomplete. Whether MetR during a specific period of adulthood increases lifespan is not shown. In Drosophila, MetR is reported to extend lifespan only when amino acid levels are low. Here, by using an exome-matched holidic medium, we show that decreasing Met levels to 10% extends Drosophila lifespan with or without decreasing total amino acid levels. MetR during the first four weeks of adult life robustly extends lifespan. MetR induces the expression of Methionine sulfoxide reductase A (MsrA) in young flies, which reduces the oxidatively-damaged Met. MsrA induction is foxo-dependent and persists for two weeks after cessation of the MetR diet. Loss of MsrA attenuates lifespan extension by early-adult MetR. Our study highlights the age-dependency of the organismal response to specific nutrient and suggests that nutrient restriction at a particular period of life is sufficient for healthspan extension.

physiology↗

bioRxiv2021

Simple and efficient differentiation of human iPSCs into contractible skeletal muscles for muscular disease modeling

Pathophysiological analysis and drug discovery targeting human diseases require disease models that suitably recapitulate patients pathology. Disease-specific human induced pluripotent stem cells (hiPSCs) can potentially recapitulate disease pathology more accurately than existing disease models when differentiated into affected cell types. Thus, successful modeling of muscular diseases requires efficient differentiation of hiPSCs into skeletal muscles. hiPSCs transduced with doxycycline-inducible MYOD1 (MYOD1-hiPSCs) have been widely used; however, they require time- and labor-consuming clonal selection procedures, and clonal variations must be overcome. Moreover, their functionality to exhibit muscular contraction has never been reported. Here, we demonstrated that bulk MYOD1- hiPSCs established with puromycin selection, but not with G418 selection, showed high differentiation efficiency, generating more than 80% Myogenin (MyoG)+ and Myosin heavy chain (MHC)+ muscle cells within seven days. Interestingly, bulk MYOD1-hiPSCs exhibited average differentiation properties compared with those of clonally established MYOD1- hiPSCs, suggesting that the bulk method may minimize the effects of clonal variations. Finally, three-dimensional muscle tissues were fabricated from bulk MYOD1-hiPSCs, which exhibited contractile force upon electrical pulse stimulation, indicating their functionality. Together, the findings indicate that our bulk differentiation requires less time and labor than existing methods, efficiently generates contractible skeletal muscles, and facilitates the generation of muscular disease models. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=167 SRC="FIGDIR/small/468571v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@12c091eorg.highwire.dtl.DTLVardef@ad1ccorg.highwire.dtl.DTLVardef@53ba90org.highwire.dtl.DTLVardef@fd65f5_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2020

Cell-cell adhesion in plant grafting is facilitated by β-1,4-glucanases

Plant grafting is conducted for vegetative propagation in plants, whereby a piece of living tissue is attached to another tissue through establishment of cell-cell adhesion. Plant grafting has a long history in agriculture and has been applied to improve crop traits for thousands of years1. Plant grafting has mostly relied on the natural ability of a plant for wound healing. However, the compatibility of cell-cell adhesion typically limits graft combinations to closely related species2-4, and the mechanism by which cell-cell adhesion of injured tissues is established is largely unknown. Here, we show that a subclade of {beta}-1,4-glucanases secreted into the extracellular region facilitates cell-cell adhesion near the graft interface. Nicotiana shows a propensity for cell-cell adhesion with a diverse range of angiosperms, including vegetables, fruit trees, and monocots, in which cell wall reconstruction was promoted in a similar manner to conventional intrafamily grafting5-7. Using transcriptomic approaches, we identified a specific clade of {beta}-1,4-glucanases that is upregulated during grafting in successful graft combinations but not in incompatible grafts and precedes graft adhesion in inter- and intrafamily grafts. Grafting was facilitated with an overexpressor of the {beta}-1,4-glucanase and, using Nicotiana stem as an interscion, we produced tomato fruits on rootstocks from other plant families. Our results demonstrate that the mechanism of cell-cell adhesion is partly conserved in plants and is a potential target to enhance plant grafting techniques.

plant biology↗

bioRxiv2019

Low temperature transcriptionally modulates natural peel degreening in lemon (Citrus limon L.) fruit independently of endogenous ethylene

AbstractPeel degreening is an important aspect of fruit ripening in many citrus fruit, and earlier studies have shown that it can be advanced either by ethylene treatment or during low temperature storage. However, the important regulators and pathways involved in natural peel degreening remain largely unknown. To understand how natural peel degreening is regulated in lemon (Citrus limon L.) fruit, flavedo transcriptome and physiochemical changes in response to either ethylene treatment or low temperature were studied. Ethylene treatment induced rapid peel degreening which was strongly inhibited by the ethylene antagonist, 1-methylcyclopropene (1-MCP). Compared with 25{degrees}C, moderately low temperatures (5{degrees}C, 10{degrees}C, 15{degrees}C and 20{degrees}C) also triggered peel degreening. Surprisingly, repeated 1-MCP treatments failed to inhibit the peel degreening induced by low temperature. Transcriptome analysis revealed that low temperature and ethylene independently regulated genes associated with chlorophyll degradation, carotenoid metabolism, photosystem proteins, phytohormone biosynthesis and signalling, and transcription factors. On-tree peel degreening occurred along with environmental temperature drops, and it coincided with the differential expression of low temperature-regulated genes. In contrast, genes that were uniquely regulated by ethylene showed no significant expression changes during on-tree peel degreening. Based on these findings, we hypothesize that low temperature plays a prominent role in regulating natural peel degreening independently of ethylene in citrus fruit. HighlightCitrus peel degreening is promoted by low temperature via modulation of multiple genes associated with chlorophyll degradation, carotenoid biosynthesis, photosystem disassembly, phytohormones and transcription factors without involving ethylene signalling.

plant biology↗

bioRxiv2019

Orientation to polarized light in tethered flying honeybees

Behavioral responses of honeybees to a zenithal polarized light stimulus were observed using a tethered animal in a flight simulator. Flight direction of the bee was recorded by monitoring the horizontal movement of its abdomen, which was strongly anti-correlated with its torque. When the e-vector orientation of the polarized light was rotated clockwise or counterclockwise, the bee responded with periodic right-and-left abdominal movements; however, the bee did not show any clear periodic movement under the static e-vector or depolarized stimulus. The steering frequency of the bee was well coordinated with the e-vector rotation frequency of the stimulus, indicating that the flying bee oriented itself to a certain e-vector orientation, i.e., exhibited polarotaxis. The percentage of bees exhibiting clear polarotaxis was much smaller under the fast stimulus (3.6 {degrees} s-1) compared with that of the slow stimulus (0.9 or 1.8 {degrees} s-1). The bee did not demonstrate any polarotactic behavior after the dorsal rim region of its eyes, which mediates insect polarization vision in general, was bilaterally covered with black paint. The bees demonstrated a high preference for e-vector orientations between 120 to 180{degrees}. Each bee exhibited similar e-vector preferences under clockwise and counterclockwise stimuli, indicating that each bee has its own e-vector preference, which probably depends on the bees previous foraging experience. Our results strongly suggest that the flying honeybees utilize the e-vector information from the skylight to deduce their heading orientation for navigation.\n\nSummary statementTethered flying bees exhibited polarotaxis under a zenithal rotating e-vector stimulus, in which their right-and-left abdominal movements were coincident with the rotation of the stimulus.

animal behavior and cognition↗