Biology subjects

Uchiyama, Y.

Publications and source records attributed to Uchiyama, Y..

10 recordsLinked to original sources

bioRxiv2024

Downregulation of astrocytic C3 production alleviates neuronal mitochondrial dysfunction in tauopathy models

Neuronal mitochondrial dysfunction is associated with cognitive decline in neurodegenerative disorders such as Alzheimers Disease (AD). In this study, multiple pieces of evidence proved that phosphorylated tau (p-Tau) caused mitochondrial swelling and dysfunction in neurons. In a novel in vitro newborn neurons culture system, we discovered mitochondrial swelling and dysfunction were associated with increased p-Tau, leading to necroptosis activation, which was induced by Complement C3 (C3) produced from activated astrocytes. In the in vivo tauopathy mouse models, the effects of astrocytic C3 on tau-associated mitochondrial dysfunction and necroptosis were also discovered in hippocampal newborn neurons, and we directly showed that p-Tau aggregation was associated with mitochondria swelling in the hippocampal neurons by electron microscopy analysis. In addition, we proved the ability of compound anserine, which can block Tak1-Ikk dependent NF-{kappa}B activation, to further down-regulate astrocytic C3 production and alleviate neuronal mitochondrial dysfunction in vitro and in vivo, respectively. Down-regulation of astrocyte C3-production by anserine could also rescue mortality as well as cognitive and motor functions. Our findings first reported the contribution of p-Tau on neuronal mitochondrial dysfunction and proposed the therapies that down-regulate astrocytic C3 production have a potential role in alleviating this neurotoxic effect.

neuroscience↗

bioRxiv2023

Endosomal-lysosomal organellar assembly (ELYSA) structures coordinate lysosomal degradation systems through mammalian oocyte-to-embryo transition

Mouse oocytes undergo drastic changes in organellar composition and their activities during maturation from the germinal vesicle (GV) to meiosis II (MII) stage. After fertilization, the embryo degrades parts of the maternal components via lysosomal degradation systems, including autophagy and endocytosis, as zygotic gene expression begins during embryogenesis. Here, we demonstrate that endosomal-lysosomal organelles form large spherical assembly structures, termed ELYSAs, in mouse oocytes. ELYSAs are observed in GV oocytes, attaining sizes up to 7-8 m in diameter in MII oocytes. ELYSAs comprise tubular-vesicular structures containing endosomes and lysosomes along with cytosolic components. Most ELYSAs are also positive for an autophagy regulator, LC3. These characteristics of ELYSA resemble those of ELVA (endolysosomal vesicular assemblies) identified independently. The signals of V1-subunit of vacuolar ATPase tends to be detected on the periphery of ELYSAs in MII oocytes. After fertilization, the localization of the V1-subunit on endosomes and lysosomes increase as ELYSAs gradually disassemble at the 2-cell stage, leading to further acidification of endosomal-lysosomal organelles. These findings suggest that the ELYSA/ELVA maintain endosomal-lysosomal activity in a static state in oocytes for timely activation during early development. Summary blurbThis study describes endosomal-lysosomal organellar assembly structures in mammalian oocytes, elucidating statistical alterations in their size, distribution, and correlation with lysosomal maturation.

developmental biology↗

bioRxiv2022

Exome-wide benchmark of difficult-to-sequence regions using short-read next-generation DNA sequencing

Next-generation DNA sequencing (NGS) in short-read mode has been recently used for genetic testing in various clinical settings. NGS data accuracy is crucial in clinical settings, and several reports regarding quality control of NGS data, focusing mostly on establishing NGS sequence read accuracy, have been published thus far. Variant calling is another critical source of NGS errors that remains mostly unexplored despite its established significance. In this study, we used a machine-learning-based method to establish an exome-wide benchmark of difficult-to-sequence regions using 10 genome sequence features on the basis of real-world NGS data accumulated in The Genome Aggregation Database (gnomAD) of the human reference genome sequence (GRCh38/hg38). We used the obtained metrics, designated "UNMET score," along with other lines of structural information of the human genome to identify difficult-to-sequence genomic regions using conventional NGS. Thus, the UNMET score could provide appropriate caveats to address potential sequential errors in protein-coding exons of the human reference genome sequence GRCh38/hg38 in clinical sequencing.

genomics↗

bioRxiv2022

DNA damage response signaling to mitochondria drives senescence

Cellular senescence is a stress-induced irreversible cell cycle arrest typically accompanied by expression of the cyclin-dependent kinase inhibitor p16INK4a (hereafter referred to as p16) and mitochondrial dysfunction1. Recent studies have indicated that p16-expressing senescent cells accumulate in the body over time and contribute to aging1, 2. Many stresses, such as telomere shortening and oncogene activation, induce senescence by damaging nuclear DNA1. However, the molecular mechanisms linking DNA damage to senescence remain unclear. Here, we show that the outer mitochondrial transmembrane protein BNIP3 drives senescence by triggering a DNA damage response (DDR) of mitochondria. BNIP3 was identified in a genome-wide siRNA screen for genes required for p16 expression upon DNA damage. Mass spectrometric analysis of BNIP3-interacting proteins yielded the DDR kinase ATM and subunits of the mitochondrial contact site and cristae organizing system (MICOS) complex. BNIP3 is an ATM substrate that increases the number of mitochondrial cristae upon DNA damage. This increase enhances the oxidation of fatty acids to acetyl-CoA, an acetyl group donor, thereby promoting histone acetylation and associated p16 expression. Our findings indicate that DDR signaling to mitochondria promotes p16 expression by altering mitochondrial structure and metabolism and highlight the importance of nuclear-mitochondrial communication in senescence induction.

cell biology↗

bioRxiv2021

Retrovirus-induced leukemia - hijack of T-cell activation mechanisms revealed by single-cell analysis

Human T-cell leukemia virus type 1 (HTLV-1) mainly infects CD4+ T-cells and induces chronic, persistent infection in infected individuals with some progressing to develop adult T-cell leukemia/lymphoma (ATL). Whilst HTLV-1 alters cellular differentiation, activation and survival, it is unknown whether and how these changes contribute to malignant transformation of infected T-cells. In this study, we used single-cell RNA-Seq and TCR-Seq to investigate T-cell differentiation and HTLV-1-mediated transformation processes. We analyzed 87,742 single cells from peripheral blood of 12 infected and 3 uninfected individuals. Using multiple independent bioinformatic methods, we demonstrated that naive T-cells dynamically change into activated T-cells including infected cells, which seamlessly transitioned into ATL cells characterized by clonally expanded, highly-activated T-cells. Notably, the more activated ATL cells are, the more they acquire Treg signatures. Intriguingly, HLA class II genes were uniquely induced in infected cells, further upregulated in ATL cells and was induced by viral protein Tax. Functional assays revealed that by upregulating HLA class II, HTLV-1-infected cells can act as tolerogenic antigen presenting cells (APCs) to induce anergy of antigen specific T-cells. In conclusion, our study revealed the in vivo mechanisms of HTLV-1-mediated transformation and immune escape at single-cell level. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=103 SRC="FIGDIR/small/458291v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@38d0fdorg.highwire.dtl.DTLVardef@20cca0org.highwire.dtl.DTLVardef@15a55e2org.highwire.dtl.DTLVardef@1bca6ac_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2021

Multi-Scale LM/EM Neuronal Imaging from Brain to Synapse with a Tissue Clearing Method, ScaleSF

The mammalian brain is organized over sizes that span several orders of magnitude, from synapses to the entire brain. Thus, a technique to visualize neural circuits across multiple spatial scales (multi-scale neuronal imaging) is vital for deciphering brain-wide connectivity. Here, we developed this technique by coupling successive light microscope/electron microscope (LM/EM) imaging with an ultrastructurally-preserved tissue clearing method, ScaleSF. Our multi-scale neuronal imaging incorporates 1) brain-wide macroscopic observation, 2) mesoscopic circuit mapping, 3) microscopic subcellular imaging, and 4) EM imaging of nanoscopic structures, allowing seamless integration of structural information from the brain to synapses. We applied the technique to three neural circuits of two different species, mouse striatofugal, mouse callosal, and marmoset corticostriatal projection systems, and succeeded in the simultaneous interrogation of their circuit structure and synaptic connectivity in a targeted way. Our multi-scale neuronal imaging will significantly advance the understanding of brain-wide connectivity by expanding the scales of objects.

neuroscience↗

bioRxiv2020

Movements of ancient human endogenous retroviruses detected in SOX2-expressing cells

Human endogenous retroviruses (HERVs) occupy approximately 8% of human genome. HERVs, which are transcribed in early embryos, are epigenetically silenced in somatic cells, except in pathological contexts. HERV-K is thought to protect the embryo from exogenous viral infection. However, uncontrollable HERV-K expression in somatic cells has been implicated in several diseases. Here, we show that SOX2, which plays a key role in maintaining pluripotency of stem cells, is critical for the transcription of HERV-K LTR5Hs. HERV-K can undergo retrotransposition within producer cells in the absence of Env expression. Furthermore, new HERV-K integration sites were identified in a long-term culture of induced pluripotent stem cells, which express SOX2. Together, these results suggest the possibility that the strict dependence of HERV-K on SOX2 have allowed contribution of HERV-K to the protection of early embryos during evolution while limiting potentially harmful effects of HERV-K retrotransposition on host genome integrity to these early embryos.

microbiology↗

bioRxiv2020

Cells recognize osmotic stress through liquid-liquid phase separation lubricated with poly(ADP-ribose)

Cells are under threat of osmotic perturbation; and cell volume maintenance is critical in cerebral edema, inflammation and aging, in which prominent changes in intracellular or extracellular osmolality emerge. After osmotic stress-enforced cell swelling or shrinkage, the cells regulate intracellular osmolality to recover their volume. However, the mechanisms recognizing osmotic stress remain obscured. We previously clarified that apoptosis signal-regulating kinase 3 (ASK3) bidirectionally responds to osmotic stress and regulates cell volume recovery. Here, we report that macromolecular crowding induces liquid-demixing condensates of ASK3 under hyperosmotic stress, which transduce osmosensing signal into ASK3 inactivation. A genome-wide small interfering RNA (siRNA) screen identified an ASK3 inactivation regulator, nicotinamide phosphoribosyltransferase (NAMPT), related to poly(ADP-ribose) signaling. Furthermore, we clarify that poly(ADP-ribose) keeps ASK3 condensates in the liquid phase and enables ASK3 to become inactivated under hyperosmotic stress. Our findings demonstrate that cells rationally incorporate physicochemical phase separation into their osmosensing systems.

cell biology↗

bioRxiv2020

Bacteroides uniformis enhances endurance exercise performance through gluconeogenesis

Athletes require high levels of energy to exercise under extreme conditions. Gut microbiota supplies energy to the host; however, the mechanism how gut microbiota contribute in the athlete is unclear. In this study, we determined that gut microbiota of Japanese long-distance runners differed from that of non-athletes, and the Bacteroides uniformis cell number in the feces correlated with 3,000-m race time. Mice administrated with B. unformis extended the swimming time to exhaustion. Furthermore, acetate and propionate concentrations in the cecum increased in B. uniformis-administered mice subjected to weekly exercise. Expression levels of carnitine palmitoyl transferase la and phosphoenolpyruvate carboxykinase genes were elevated in the liver, suggesting that acetate and propionate produced by B. uniformis improve endurance exercise performance, at least in part, through enhancing gluconeogenesis. In addition, -cyclodextrin administration increased B. uniformis and improved the performance in humans and mice, thus it is a candidate substance enhancing exercise performance through modification of gut microbiota.

microbiology↗

bioRxiv2019

Toxicokinetics of citreoviridin in vivo and in vitro.

Citreoviridin (CIT) produced by Penicillium citreonigrum as a secondary metabolite is a yellow rice toxin that has been reported to be related to acute cardiac beriberi; however, its toxicokinetics remain unclear. The present study elucidated the toxicokinetics through swine in vivo experiments and predicted the human toxicokinetics by a comparison with findings from in vitro experiments. Swine in vivo experiments revealed that CIT had a high bioavailability of more than 90%. In addition, it showed a large volume of distribution (1.005 {+/-} 0.195 L/kg) and long elimination half-life (17.7 {+/-} 3.3 h) in intravenous. These results suggested the possibility of a slow metabolism of CIT. An intestinal permeability study using the human cell line Caco-2 showed that CIT had a high permeability coefficient, suggesting it would be easily absorbed in human intestine, similar to its absorption in swine. The metabolite profiles were investigated by incubating CIT with S9 obtained from swine and humans. Hydroxylation, methylation, desaturation and dihydroxylation derivatives were detected as the predominant metabolites, and CIT glucuronide was produced slowly compared with above metabolites. A comparison of the peak area ratios obtained using quadrupole time-of-flight mass spectrometer showed that the rates of all of the main metabolites except for glucuronide produced using human S9 were three-fold higher than those obtained using swine S9. Furthermore, the elimination of CIT using human S9 was more rapid than when using swine S9, indicating that CIT would be metabolized faster in humans than in swine. These in vivo results suggested that CIT is easily absorbed in swine and persists in the body for a long duration. Furthermore, the CIT metabolism appeared to be faster in human liver than in swine liver in vitro, although the bioavailability of CIT was predicted to be similarly high in humans as in swine.

pharmacology and toxicology↗