Biology subjects

Sato, T.

Publications and source records attributed to Sato, T..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

Non-DNA-damaging DNA-PK activation improving hearing and prolonging life due to NAD+ and SIRT upregulation

Emerging evidence strongly supports a close relationship between age-related hearing loss and frailty, highlighting the importance of early detection and intervention. Recently, we invented a mitochondria-homing drug named mitochonic acid 5 (MA-5), that increases the adenosine triphosphate (ATP) levels, rescue mitochondrial function, and protect tissue damages. Currently, the phase I clinical trial has been finished in Japan (jRCT2031210495) and the phase 2 clinical trial has already been approved by PMDA. Here we show that MA-5 improved various types of hearing loss in mouse models. Structural chemical bioanalysis revealed that MA-5 is a mixture of equal amount of S- and R- enantiomer and both S- and R- enantiomer increase ATP by binding mitochondrial protein, mitofilin. However, S-enantiomer significantly increased the NAD+ levels by binding to the NAD+-producing key enzyme nicotinamide phosphoribosyltransferase (NAMPT). Moreover, the S-enantiomer increased the sirtuin 1 protein by suppressing polyubiquitination induced by tripartite motif containing 28 (TRIM28) phosphorylation which was triggered by DNA-dependent protein kinase (DNA-PK) activation in the absence of DNA damage. Transcriptomic signatures showed that the signature of MA-5 shows an inverse correlation with aging and mortality and is oriented in the same direction as the OSKM-related iPSCs, suggesting the modification of aging pathways. Oral administration of MA-5 to mitochondrial disease model mouse showed increased survival. Our findings suggest that, in addition to enhancing ATP levels, the coordinated regulation of NAD+ metabolism, SIRT protein expression, and DNA-PK activity-constituting a novel therapeutic triad may contribute to the amelioration of hearing impairment and mitochondrial dysfunction, thereby improving life prognosis.

cell biology↗

bioRxiv2025

Repressive S-adenosylmethionine biosynthesis status inhibits transcription of HeT-A retrotransposon in the germline of Drosophila.

S-adenosylmethionine (SAM) is the principal cellular donor of methyl moiety in the methylation reaction and regulates gene expression by regulating methylation-related cellular events, such as epigenetic status. Although SAM biosynthesis affects a variety of biological phenomena including disease and aging, whether cell-specific SAM biosynthesis status is present and how it contributes to cellular function are largely unknown. Here, we firstly showed that the Drosophila germline in gametogenesis has a repressive SAM biosynthesis status through the observation of SAM synthetase (Sam-S), a key enzyme for SAM biosynthesis. In addition, our study showed that germline-unique repressive SAM biosynthesis status contributes to inhibition of retrotransposon expression; enhancement of SAM biosynthesis in germline caused excessive expression of retrotransposons including HeT-A, a telomere-specific retroelement, as the most affected target. We found that the promoter activity of HeT-A is enhanced in SAM increased condition with increased accumulation of 6mA DNA methylation, the major DNA methylation modification in the Drosophila genome. Interestingly, the enhanced 6mA enrichment and gene expression in enriched loci were not correlated in other retrotransposons or structural genes. Taken together, our results suggest that SAM-deficient status in the germline uniquely regulates HeT-A transcription via 6mA methylation modification. Thus, our study provides a new understanding of how germline unique metabolic status contributes to regulation of the retrotransposon.

developmental biology↗

bioRxiv2025

Integration of Proxy Intermediate Omics traits into a Nonlinear Two-Step model for accurate phenotypic prediction

Intermediate omics traits, which mediate the effects of genetic variation on phenotypic traits, are increasingly recognised as valuable components of genetic evaluation. In particular, rhizosphere microbiota play a crucial role in plant health and productivity; however, their complex interactions with host genetics remain challenging to model. Although two-step modeling frameworks have been proposed to integrate intermediate omics traits into phenotype prediction, existing approaches do not incorporate nonlinear relationships between different omics layers. To address this, we have proposed a two-step phenotype prediction framework that integrates genomic, rhizosphere microbiome, and metabolome (meta-metabolome) data, while explicitly capturing omicsomics nonlinearities. The first step is to predict meta-metabolome traits from genetic and microbial features, thus effectively isolating them from the environmental noise. In this process, intermediate "proxy" omics traits are generated as general biological information to provide robust models. The second step utilises this "proxy" to enhance the accuracy of the phenotype prediction. We compared the linear model (Best Linear Unbiased Prediction, BLUP) and the nonlinear model (Random Forest, RF) at each step, as demonstrated through simulations and empirical analysis of a multi-omics soybean dataset in which nonlinear modeling captures intricate omics interactions. Notably, our approach enables phenotype prediction without requiring the original meta-metabolome data used in model training, thereby reducing reliance on costly omics measurements. This framework integrates intermediate omics traits into genomic prediction to improve prediction accuracy and provide solutions for deeper insights into plant-microbiome interactions.

bioinformatics↗

bioRxiv2025

First evidence of Clavicipitaceous fungus attacking a vertebrate

Metapochonia bulbillosa (Clavicipitaceae) was isolated as a causative agent of a new frog mycosis of Pelophylax porosus brevipodus, one of the endangered frogs in Japan. Analysis of spontaneous outbreaks and infection experiments confirmed that the fungus can lethally affect Pelophylax porosus brevipodus, as well as Dryophytes japonicus. This is the first evidence that a species of Clavicipitaceae, originally known as a plant pathogen, also affects vertebrates.

microbiology↗

bioRxiv2025

Protein Secretion From Liver Ex Vivo Reveals Regulation of Hepatokines by Sex and Circadian Rhythm

Here, we use an ex vivo approach compatible with the circadian timescale to interrogate protein secretion from liver, revealing several findings. Proteomic analyses in male and female mice identify hundreds of proteins that exhibit time-of-day-dependent or clock-dependent secretion involved in extracellular matrix, immune, redox, xenobiotic, and fatty acid functions. Among these, the liver secretes more endostatin, a cleavage product of collagen type XVIII alpha 1 (COL18A1), during the inactive, fasting phase of the diurnal cycle. Temporal regulation of COL18A1/endostatin is dysregulated upon loss of Bmal1 through combined effects on Col18a1 transcriptional repression and proteolytic processing. Functional experiments in vivo and in vitro reveal that endostatin suppresses mitochondrial gene expression in white adipose tissue in a time-dependent manner and reduces mitochondrial respiration in adipocytes, while enhancing lipolysis. These results support a mechanism of inter-organ crosstalk whereby hepatically derived, temporally-restricted endostatin tunes adipocytes toward metabolic activities required during the fasting phase.

molecular biology↗

bioRxiv2025

Discovery of The Clinical Candidate S-892216: A Second-Generation of SARS-CoV-2 3CL Protease Inhibitor for Treating COVID-19

The coronavirus disease 2019 (COVID-19) pandemic crisis has been mitigated by worldwide efforts to develop vaccines and therapeutic drugs. However, there remains concern regarding public health and an unmet need for therapeutic options. Herein, we report the discovery of S-892216, a second-generation SARS-CoV-2 3C-like protease (3CLpro) inhibitor, to treat COVID-19. S-892216 is a reversible covalent 3CLpro inhibitor with highly potent antiviral activity and an EC50 value of 2.48 nM against SARS-CoV-2 infected cells. Structure-based design of a covalent modifier for compound 1 revealed that introducing a nitrile warhead increased 3CLpro inhibition activity by 180-fold. Subsequent optimization efforts yielded S-892216, which combined a favorable pharmacokinetic profile and high off-target selectivity. S-892216 exhibited antiviral activity against diverse SARS-CoV-2 variants, with no cross-resistance to major mutations reducing antiviral activities of nirmatrelvir and ensitrelvir. In SARS-CoV-2-infected mice, S-892216 inhibited viral replication in the lungs similar to ensitrelvir, although at a 30-fold lower dose.

biochemistry↗

bioRxiv2025

Glucagon dysfunction in the liver induces hyperplasia of PP cells and the production of glucagon and pancreatic polypeptide double-positive cells

Understanding the mechanisms that regulate cellular identity and proliferation is crucial for elucidating cellular functions. Under normal conditions, pancreatic endocrine cells express only a single hormone, and their numbers are tightly regulated. Contrary to this general principle, our study revealed a significant increase in glucagon (GCG) and pancreatic polypeptide (PP) double-positive cells (GCG+ PP+ double-positive cells), along with hyperplasia of both PP and cells in proglucagon-deficient mice. Similarly, systemic glucagon receptor-deficient mice exhibited PP-cell hyperplasia and an increase in GCG+ PP+ double-positive cells, with enhanced PP-cell self-replication observed at 4 weeks and the appearance of GCG+ PP+ double-positive cells at 10 weeks. Liver-specific glucagon receptor-deficient mice induced similar effects, which were linked to hyperaminoacidemia. Elevated glutamine levels were found to promote GCG+ PP+ double-positive cell formation via mTOR signaling, suggesting a molecular mechanism driving pancreatic endocrine cell plasticity. Collectively, these findings indicate that increased plasma amino acid levels caused by impaired glucagon action in the liver promotes the proliferation of cells and PP cells, and disturbs their cellular identity maintenance.

cell biology↗

bioRxiv2025

A bright synthetic near-infrared luciferin enhances the capabilities of deep-tissue bioluminescence imaging using firefly luciferases

Synthetic bioluminescence reactions exhibiting near-infrared (NIR)-shifted spectra have been explored to improve deep-tissue imaging through the design of firefly luciferin analogues. Although the NIR bioluminescence reactions improve the tissue penetration of bioluminescence signals from deep tissues, their photon output is markedly lower compared to the natural reaction with D-luciferin and firefly luciferase (Fluc), often by an order of magnitude or more. Consequently, in most instances, the sensitivity of NIR bioluminescence imaging (NIR-BLI) has not yet substantially surpassed that of BLI with the natural firefly reaction. Here, we present a synthetic firefly luciferin, named AkaSuke, that generates intense NIR bioluminescence ({lambda}max = 680 nm) in reaction with Fluc, greatly improving the detection sensitivity beyond that of the D-luciferin/Fluc reaction for targeting deep tissue. AkaSuke enables sensitive visualizations of ectopic hematogenesis through entire tissues of mice over time following transplantation of bone marrow stem cells labeled with Fluc. We additionally identify a Japanese firefly luciferase, DkumLuc1, that displays higher catalytic activities for bioluminescence emission of AkaSuke compared to typical Fluc, resulting in detection sensitivity comparable to that of AkaLumine/Akaluc reaction, one of the most sensitive bioluminescence systems for deep tissue imaging. We further propose the potential of the AkaSuke/DkumLuc1 reaction as an orthogonal pair with the AkaLumine/Akaluc for sensitive dual-target tracking in mice. Overall results suggest that AkaSuke enhances the capabilities of deep-tissue bioluminescence imaging using Fluc and its variant, and could serve as an emerging benchmark for the molecular design of NIR luciferin analogues.

cancer biology↗

bioRxiv2025

Scg2 drives reorganization of the corticospinal circuit with spinal premotor interneurons to recover motor function after stroke

Brain injuries such as stroke damage neural circuitry and lead to functional deficits. Spared motor pathways are often reorganized and contribute to functional recovery; however, the connectivity and molecular mechanisms that drive the reorganization are largely unknown. Here, we demonstrate structural and functional connectivity reformed by spared corticospinal axons after stroke and determine a key secretory protein that drives the reorganization. We first found that corticospinal axons innervate specific areas of the denervated cervical cord after stroke. Anatomical and photometric analyses reveal that the axons reconnect to premotor V2a interneurons. Kinematic analyses of forelimb movements and chemogenetic silencing reveal their contribution to motor recovery. Translated mRNA expression analyses of V2a interneurons and astrocytes in the denervated cervical cord reveal diverse transcripts upregulated in the rewiring process. In particular, a secretory protein Scg2 is upregulated by injury-induced purinergic ATP signals and rehabilitative training-induced neural activity and possesses an ability to promote axon growth via cAMP and S6 signaling. Scg2 overexpression in the denervated cervical cord enhances axon rewiring, while the Scg2 knockdown attenuates it. The present data reveal the neural substrate and molecular mechanism essential to induce reorganization and recovery of the motor system, providing fundamental therapeutic targets for CNS injuries.

neuroscience↗

bioRxiv2025

The liver clock tunes transcriptional rhythms in skeletal muscle to regulate mitochondrial function

Circadian clocks present throughout the brain and body coordinate diverse physiological processes to support daily homeostasis and respond to changing environmental conditions. The local dependencies within the mammalian clock network are not well defined. We previously demonstrated that the skeletal muscle clock controls transcript oscillations of genes involved in fatty acid metabolism in the liver, yet whether the liver clock also regulates the muscle was unknown. Here, we use hepatocyte-specific Bmal1 KO mice (Bmal1hep-/-) and reveal that approximately one third of transcriptional rhythms in skeletal muscle are regulated by the liver clock vivo. Treatment of myotubes with serum harvested from Bmal1hep-/- mice inhibited expression of genes involved in metabolic pathways, including oxidative phosphorylation. Overall, the transcriptional changes induced by liver clock-driven endocrine-communication revealed from our in vitro system were small in magnitude, leading us to surmise that the liver clock acts to fine-tune metabolic gene expression in muscle. Strikingly, treatment of myotubes with serum from Bmal1hep-/- mice inhibited mitochondrial ATP production compared to WT and this effect was only observed with serum harvested during the active phase. Overall, our results reveal communication between the liver clock and skeletal muscle-uncovering a bidirectional endocrine communication pathway dependent on clocks in these two key metabolic tissues. Targeting liver and muscle circadian clocks may represent a potential avenue for exploration for diseases associated with dysregulation of metabolism in these tissues.

cell biology↗

bioRxiv2024

Confinement stress with movement restriction suppresses male courtship in Drosophila through dopamine-dependent neuroplasticity

Stress disturbs the physiological and psychological balance in animals, leading to changes in brain function. Here, we show that stress in a small space with movement restriction (SS stress) suppresses male courtship in Drosophila and that alterations in dopamine signaling induced by SS stress are responsible for the persistence of this suppression after the stress experience. We found that SS stress activates numerous dopamine neurons in the brain. Pharmacological and genetic analyses revealed that dopamine synthesis, release, and reception are essential for the persistence of SS-stress-induced courtship suppression. A specific subset of dopamine neurons projects to the mushroom body (MB), a brain region where various sensory inputs are integrated. We identified that SS-stress-induced dopamine release plastically depresses the activity of a subset of MB neurons, and this neuronal depression contributes to the sustained suppression of male courtship behavior following stress exposure. This novel stress model using Drosophila provides valuable insights into dopamine-mediated stress mechanisms, particularly those related to confined spaces.

neuroscience↗

bioRxiv2024

Interparental Gene Conversion in General Population: A Novel Mechanism For Loss of Heterozygosity

Gene conversion is a process in which genetic material from a donor sequence is unidirectionally copied to an acceptor sequence during the homologous recombination repair of a DNA double-strand break. Although gene conversion has been widely studied in the context of meiosis, hereditary diseases, and cancer development, gene conversion between parental homologs in the zygotes remains controversial. Here, we developed a method to detect interparental gene conversions by focusing on Mendelian errors and identified gene conversion events in one out of every 21.8 births. Some of these events were observed in genetic regions, potentially affecting offspring phenotypes. Interparental gene conversion leads to the offspring inheriting two identical alleles from one parent, resulting in a loss of heterozygosity. Our findings suggest that naturally occurring interparental gene conversions may provide a novel mechanism for the development of certain genetic diseases.

genomics↗

bioRxiv2024

Self-organization of spermatogenic wave coordinates sustained sperm production in the mouse testis

Spermatogenesis takes place in the testis, relying on the ordered turnover of differentiating cells supplied from stem cells. Classic histological analyses have revealed that this process shows hierarchical spatiotemporal patterning known as the spermatogenic cycle, wave, and descent of segmental order, indicative of currently underexplored mechanisms of tissue- and organ-scale homeostasis. Here, using mice, we conducted high-resolution, wide-field, and ultra long-term live imaging studies in vivo and ex vivo, combined with whole-organ mapping of differentiation stages. Such trans-scale measures demonstrate how stereotypic local cell turnover is coordinated into characteristic phase waves propagating along the seminiferous tubules, further organized into organ-scale patterning over the tubule loops. Minimal mathematical modeling shows that such higher-order dynamics can emerge from the local coupling of autonomous oscillators, which are rooted in delayed feedback interplay between stem and differentiating cells via retinoic acid signaling. These findings highlight a self-organization mechanism underpinning organ-scale homeostasis and constant sperm production.

developmental biology↗

bioRxiv2024

Isotonic and minimally invasive optical clearing media for live cell imaging ex vivo and in vivo

Tissue clearing has been widely used for fluorescence imaging of fixed tissues, but not for live tissues due to its toxicity. Here we develop minimally invasive optical clearing media for fluorescence imaging of live mammalian tissues. Light scattering is minimized by adding spherical polymers with low osmolarity to the extracellular medium. A clearing medium containing bovine serum albumin (SeeDB-Live) is minimally invasive to live cells, allowing for structural and functional imaging of live tissues, such as spheroids, organoids, acute brain slices, and the mouse brain in vivo. SeeDB-Live minimally affects the electrophysiological properties and sensory responses of neurons. We demonstrate its utility for widefield imaging of subcellular voltage dynamics, such as backpropagating action potentials, in acute brain slices. We also utilize SeeDB-Live for widefield voltage imaging of dozens of dendrites in vivo, demonstrating population dynamics. Thus, SeeDB-Live expands the scale and modalities of fluorescence imaging of live mammalian tissues.

neuroscience↗

bioRxiv2024

An in vitro modelling of resolving macrophage with Raw 264.7 macrophage cell line

In acute inflammation, macrophages polarises its phenotype in order to participate effectively in the inflammatory, anti-inflammatory and resolving phases. Particularly, the resolving phase is vital for homeostatic recovery. The in vivo murine peritonitis model had identified various subtypes of resolving macrophages. However, the in vivo model has limitations in deciphering the molecular mechanisms required for resolving macrophage polarisation. Therefore the aim of this study is to establish an in vitro model that could simplify the reproduction of resolving macrophage polarisation. This model will be a useful tool to screen for molecular mechanisms essential for triggering resolution. Our in vitro model showed Raw 264.7 cells exhibited classical inflammatory-like (M1-like) phenotype between 2-24 h with increased interleukin-1{beta} expression and tumour necrosis factor- secretion. Concurrently, at 22-24 h there was an increase in Raw 264.7 cells polarising to anti-inflammatory like (M2-like) phenotype. These M2-like macrophages were increased in arginase activity and interleukin-10 expression. By 48 h, Raw 264.7 cells were polarised to resolving-like (Mres-like/CD11blow) phenotype. These macrophages were characterised by high efferocytic index and a decrease in inflammatory cytokine expression, low arginase activity and low CD11b expression. In summary, this in vitro resolution model showed resolving-like polarisation in a macrophage cell line.

cell biology↗

bioRxiv2024

ZIP13 regulates lipid metabolism by changing intracellular iron and zinc balance

Metabolic diseases are caused by a prolonged energy imbalance, and adipose tissue is known to be the main contributor. We previously reported that ZIP13, an Slc39a transporter whose deficiency causes Ehlers-Danlos syndrome spondylocheirodysplastic type 3 associated with lipoatrophy, inhibits the adipocyte browning pathway by modulating intracellular zinc status. The precise mechanisms of how ZIP13 regulates the homeostasis of adipose tissue remain unclear and therefore, we investigated the role of ZIP13 in mature adipocytes using adipocyte-specific Zip13-deficient mice. We herein demonstrate that these mice show accelerated lipolysis and reduced respiratory exchange ratio. In addition, abundance of iron and zinc balance were altered during differentiation in normal adipocytes, whereas iron distribution was substantially affected in Zip13-deficient adipocytes, which downregulated PDE activity and enhanced {beta}-adrenergic receptor signaling pathways. Importantly, we confirmed that ZIP13 could transport both zinc and iron, using the Xenopus oocyte transport system and in silico structural dynamics simulations, and that the defect in iron distribution perturbs proper lipolysis. Together, these results illustrate that ZIP13 acts as a key regulator for lipolysis in adipocytes via the proper use of metals, and that the ZIP13-iron axis plays an important role in regulation of lipid metabolism.

cell biology↗

bioRxiv2024

Regulation of intracellular cAMP levels in osteocytes by mechano-sensitive focal adhesion kinase via PDE8A

Osteocytes are the primary mechano-sensitive cell type in bone. Mechanical loading is sensed across the dendritic projections of osteocytes leading to transient reductions in focal adhesion kinase (FAK) activity. Knowledge regarding the signaling pathways downstream of FAK in osteocytes is incomplete. We performed tyrosine-focused phospho-proteomic profiling in osteocyte-like Ocy454 cells to identify FAK substrates. Gs, parathyroid hormone receptor (PTH1R), and phosphodiesterase 8A (PDE8A), all proteins associated with cAMP signaling, were found as potential FAK targets based on their reduced tyrosine phosphorylation in both FAK- deficient or FAK inhibitor treated cells. Real time monitoring of intracellular cAMP levels revealed that FAK pharmacologic inhibition or gene deletion increased basal and GPCR ligand-stimulated cAMP levels and downstream phosphorylation of protein kinase A substrates. Mutating FAK phospho-acceptor sites in Gs and PTH1R had no effect on PTH- or FAK inhibitor-stimulated cAMP levels. Since FAK inhibitor treatment augmented cAMP levels even in the presence of forskolin, we focused on potential FAK substrates downstream of cAMP generation. Indeed, PDE8A inhibition mimicked FAK inhibition at the level of increased cAMP, PKA activity, and expression of cAMP-regulated target genes. In vitro kinase assay showed that PDE8A is directly phosphorylated by FAK while immunoprecipitation assays revealed intracellular association between FAK and PDE8A. Thus, FAK inhibition in osteocytes acts synergistically with signals that activate adenylate cyclase to increase intracellular cAMP. Mechanically-regulated FAK can modulate intracellular cAMP levels via effects on PDE8A. These data suggest a novel signal transduction mechanism that mediates crosstalk between mechanical and cAMP-linked hormonal signaling in osteocytes.

molecular biology↗

bioRxiv2024

Stable platelet production via the bypass pathway explains the long-term reconstitution capacity of hematopoietic stem cells

Precise understanding how hematopoietic stem cells (HSCs) differentiate in vivo is difficult because we can not trace the in vivo differentiation of HSCs. The single-cell transplantation assay and our own paired daughter cell assay of phenotypic HSCs has revealed the presence of HSCs with reconstitution capacity whose differentiation potential is restricted to the myeloid lineage (MySCs) and the presence of novel direct differentiation pathway form HSCs to MySCs (named myeloid bypass pathway). However, how HSCs differentiate in vivo during hematopoiesis has remained unclear since the paired daughter cell assay was performed partially ex vivo. Aiming to characterize HSCs, including the myeloid bypass pathway, we examined the kinetics of HSC differentiation using a mathematical model. We analyzed data from single-cell transplantation assays in which five blood cell lineages were followed successively after transplantation. An age-related skewing to the myeloid lineage was quantitatively indicated as the production of B cells reduced with age. Dependence on platelet bypass increased with aging and consistently high dependence was associated with long-term reconstitution capacity of the HSCs. Focusing on the ratio of chimerism among cell lineages, the characteristics of dependence on platelet bypass can be accurately determined by the ratio of erythrocyte to platelet chimerism at 8 weeks after transplantation. This new identification criterion is an indicator of long-term reconstitution of HSCs that does not rely on observation of long-term transplantation experiments. These findings reveal the novel characteristics of HSCs related to aging and stemness and highlight the importance of the bypass pathway in HSC differentiation. Significance statementIn vivo differentiation of hematopoietic stem cells (HSCs) is important for understanding blood cell production. Here we investigated the differentiation kinetics of HSCs in single-cell transplantation assays by using a mathematical model. Our findings demonstrate the importance of the bypass pathway in platelet production for the long-term reconstitution capacity of HSCs. These results also suggest the utility of studying time changes in HSC differentiation. The new HSC characteristics and its detection criteria identified in this study are expected to be useful in understanding HSC diversity and aging.

cell biology↗