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Biology subjects

Fujii, M.

Publications and source records attributed to Fujii, M..

At least 19 recordsLinked to original sources

A PKD-caveolin axis drives secretory carrier biogenesis at the TGN

Constitutive secretion from the trans-Golgi network (TGN) to the cell surface proceeds via carriers thought to form without a canonical cytoplasmic coat, yet how these carriers are generated remains poorly understood. Here, we identify a distinct population of TGN-to-cell surface carriers transporting influenza hemagglutinin (HA) and uncover a coat-like mechanism underlying their formation. HA carrier biogenesis requires non-vesicular lipid transfer at endoplasmic reticulum (ER)-Golgi membrane contact sites (MCSs) and protein kinase D (PKD) activity. We show that caveolin promotes membrane budding by assembling into cholesterol- and PKD-associated oligomers that act as a membrane-embedded, coat-like scaffold at lipid nanodomain-enriched TGN subdomains. These findings establish caveolin as a structural and regulatory component of TGN export and support a model in which a PKD-caveolin axis couples ER-Golgi lipid transfer to cargo sorting, membrane remodeling and fission during secretory carrier biogenesis.

cell biology↗

PEG10-ORF1 programs trophoblast progenitor development for placental labyrinth formation

The emergence of the placenta was a significant event in mammalian evolution, enabling therian mammals to give birth to live young through viviparity. A key genomic change associated with this process was likely the acquisition of the therian-specific paternally expressed 10 (PEG10) from a metavirus, as Peg10-null mutant mice exhibit early embryonic lethality due to the absence of both the spongiotrophoblast and labyrinth layers in the placenta. PEG10 encodes a GAG-like open reading frame 1 (ORF1) and a POL-like ORF2, and produces two proteins, PEG10-ORF1 and PEG10-ORF1/2 fusion proteins, via the -1 frameshift mechanism conserved in retroviruses and metaviruses. Here, we demonstrate PEG10-ORF1 plays an essential and distinct role in labyrinth development. Mice lacking ORF1 but retaining the ORF1/2 protein initially developed normally in both embryos and placentas; however, later exhibited underdevelopment of the placental labyrinths complex microarchitecture, accompanied by mid-to late gestational growth retardation and lethality. These severe defects are most likely attributable to dysregulated development of labyrinth trophoblast precursor (LaTP) cells. Beyond its essential role in early placental formation, we previously demonstrated that the DSG protease domain within PEG10-ORF1/2--a metaviruse-derived feature--is critical for maintaining fetal capillaries during late gestation. Thus, PEG10 fulfills multiple indispensable functions in placental formation and maintenance by exploiting a metavirus-derived multi-protein and -peptide production system, despite being a single gene. This study provides additional evidence underscoring the profound role of PEG10 acquisition in therian placental evolution. Significance StatementThe placenta is an essential organ for viviparous reproduction in therian mammals; therefore, its evolutionary emergence is of significant interest. One key event may have been the acquisition of PEG10, a metavirus (retrovirus-like LTR retrotransposon)- derived gene, by the common therian ancestor. We previously showed that Peg10 is required for early placental development and that its protease domain is essential for late-gestational maintenance of fetal capillaries within the placental labyrinth. Here, we provide additional genetic evidence that Peg10 is also indispensable for mid-gestational development of the placental labyrinthine microvasculature. Together, these findings illustrate how multiple, stage-specific functions of a single metavirus-derived gene, PEG10, coordinate placental formation and maintenance, highlighting the evolutionary importance of PEG10 acquisition in therian placentation.

developmental biology↗

Development of ENTV reverse genetics system and phenotypic evaluation of rescued virus reveals host-specific replication patterns in mosquitoes

Entebbe bat virus (ENTV) is a bat-associated flavivirus with no known vector. Research into the biology of this virus, including assessment of the possibility that it may be vector-transmitted, is hindered by a lack of molecular tools and robust genetic systems. Therefore, we sequenced the complete 3 untranslated region, which was not previously available, and developed an infectious clone of ENTV to facilitate further investigation of the virus. Virus derived from the clone replicated similarly to the parental virus isolate in various vertebrate cells. Surprisingly, ENTV replicated to high titers in Aedes aegypti and Aedes albopictus mosquito cell lines, but there was no replication or infection in Culex tarsalis cells. In addition, phylogenetic and bioinformatics analyses strongly suggested that ENTV may be associated with a mosquito host. Given the bioinformatics support and efficient growth in Aedes cells, we orally exposed Ae. aegypti and Ae. albopictus to ENTV to evaluate infection. The ENTV blood-fed mosquitoes were all negative for infection; however, when ENTV was intrathoracically inoculated, bypassing the initial midgut infection and escape barriers, it replicated to high levels in the body, without dissemination of infectious virus into the saliva. These findings suggest that, despite demonstrating high molecular compatibility at the cellular level in Aedes mosquitoes, Ae. aegypti and Ae. albopictus are unlikely to serve as competent vectors for ENTV transmission due to strong midgut infection barriers. The clone presented in this manuscript should help to clarify the mechanisms for transmission and maintenance of ENTV, which remain poorly understood.

microbiology↗

Disturbed proteostasis is the key event that triggers cellular senescence through the regulation of chromatin organization and genome stability

Mammalian cells undergo irreversible proliferation arrest when exposed to stresses, a phenomenon termed cellular senescence. Various types of stress induce cellular senescence; nonetheless, senescent cells show similar phenotypes overall. Thus, cells undergo cellular senescence through the similar mechanisms, regardless of the type of stress encountered. Here we aimed to reveal the mechanisms underlying cellular senescence. We have previously shown that lamin b receptor (LBR), which is a protein that regulates heterochromatin organization, was downregulated in senescent cells, and downregulation of LBR induced cellular senescence. Additionally, we have shown that downregulation of protein synthesis effectively suppressed cellular senescence. Thereby, chromatin organization and protein synthesis are implicated in the regulation of cellular senescence. We examined the roles of them in cellular senescence and found that protein synthesis was upregulated during the induction of cellular senescence, and upregulated protein synthesis caused disturbed proteostasis that led to the decreased function of LBR. Furthermore, we showed that decreased LBR function induced cellular senescence through altered chromatin organization and increased genome instability. Importantly, these findings revealed a link between protein synthesis and chromatin organization and accounted for the phenotypes of senescent cells which show disturbed proteostasis, altered chromatin organization, and increased genome instability. Our findings provided the general model for the mechanisms of cellular senescence.

cell biology↗

Parasitoid wasp venoms degrade Drosophila imaginal discs for successful parasitism

Parasitoid wasps, one of the most diverse and species-rich animal taxa on Earth, produce venoms that manipulate host development and physiology to exploit host resources. However, mechanisms of venom action remain poorly understood. Here, we show that infection of host Drosophila by the endoparasitoid wasp, Asobara japonica, triggers imaginal disc degradation (IDD) by inducing apoptosis, autophagy, and mitotic arrest, leading to impaired host metamorphosis. A multi-omics approach identified two venom proteins of A. japonica necessary for IDD. Knockdown experiments targeting the venom genes revealed that in concert with host immune suppression, IDD is essential for successful parasitism. Our study highlights a venom-mediated hijacking strategy of the parasitoid wasp that allows host larvae to grow, but ultimately kills the hosts.

developmental biology↗

MicroRNA-27a-5p downregulates the expression of proinflammatory cytokines in lipopolysaccharide-stimulated human dental pulp cells via NF-κB signaling pathway

AimTo investigate the effect of microRNA-27a-5p (miR-27a-5p) on the expression of proinflammatory cytokines in human dental pulp cells (hDPCs) stimulated by lipopolysaccharide (LPS). MethodologyExpression of miR-27a-5p was evaluated in LPS-stimulated hDPCs isolated from third molars of healthy patients by a TaqMan microRNA assay. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and a cytometric bead array were used to measure mRNA and protein expression levels, respectively, of proinflammatory cytokines interleukin (IL)-6, IL-8, and monocyte chemotactic protein 1 (MCP1). Luciferase assays and western blotting were conducted to assess nuclear factor {kappa}B (NF-{kappa}B) activity. Gene/protein expression of NF-{kappa}B signaling activators, i.e., transforming growth factor beta-activated kinase 1 binding protein 1 (TAB1), IL-1 receptor-associated kinase 4 (IRAK4), NF-{kappa}B p65 (RELA), and follistatin-like 1 (FSTL1), was evaluated by RT-qPCR and western blotting. Transfection of an miR-27a-5p mimic was performed using Lipofectamine RNAiMax reagent. Wildtype and mutated 3{square}-untranslated region (UTR) of TAB1-contained luciferase reporter vectors were co-transfected with the miR-27a-5p mimic. Small interfering RNA against TAB1 (siTAB1) was designed to block its expression. One-way analysis of variance and Students t-test were used to determine statistical significance ( = .05). ResultsLPS-stimulated hDPCs showed concurrent increases in the expression of miR-27a-5p and proinflammatory cytokines (IL-6, IL-8, and MCP1), and the increased expression was suppressed by NF-{kappa}B inhibitor BAY 11-0785. Transfection of the miR-27a-5p mimic downregulated expression of proinflammatory cytokines, NF-{kappa}B activity, and expression of NF-{kappa}B signaling activators (TAB1, IRAK4, RELA, and FSTL1) in LPS-stimulated hDPCs. Luciferase reporter assays revealed that miR-27a-5p bound directly to the 3{square}-UTR of TAB1. siTAB1 downregulated NF-{kappa}B activity and proinflammatory cytokine expression. Downregulation of proinflammatory cytokine expression, NF-{kappa}B activity, and NF-{kappa}B signaling activator expression (TAB1, IRAK4, and RELA) was also found in LPS-stimulated rat incisor pulp tissue explants following transfection with the miR-27a-5p mimic ex vivo. ConclusionsMiR-27a-5p, whose expression was induced by NF-{kappa}B signaling, negatively regulated the synthesis of proinflammatory cytokines via targeting NF-{kappa}B signaling. In particular, TAB1, a potent NF-{kappa}B activator, was targeted by miR-27a-5p. These results provide insights into the negative regulatory effects of miR-27a-5p, particularly those targeting the TAB1-NF-{kappa}B signaling pathway, on pulp inflammation.

pathology↗

In vivo transomic analyses of glucose-responsive metabolism in skeletal muscle reveal core differences between the healthy and obese states

Metabolic regulation in skeletal muscle is essential for blood glucose homeostasis. Obesity causes insulin resistance in skeletal muscle, leading to hyperglycemia and type 2 diabetes. In this study, we performed multiomic analysis of the skeletal muscle of wild-type (WT) and genetically obese (ob/ob) mice, and constructed regulatory transomic networks for metabolism after oral glucose administration. Our network revealed that metabolic regulation by glucose-responsive metabolites had a major effect on WT mice, especially carbohydrate metabolic pathways. By contrast, in ob/ob mice, much of the metabolic regulation by glucose-responsive metabolites was lost and metabolic regulation by glucose-responsive genes was largely increased, especially in carbohydrate and lipid metabolic pathways. We present some characteristic metabolic regulatory pathways found in central carbon, branched amino acids, and ketone body metabolism. Our transomic analysis will provide insights into how skeletal muscle responds to changes in blood glucose and how it fails to respond in obesity.

systems biology↗

Mathematical model of chromosomal dynamics during DNA double strand break repair in budding yeast

During the repair of double-strand breaks (DSBs) in DNA, active mobilizations for conformational changes in chromosomes have been widely observed in eukaryotes, from yeast to animal and plant cells. DSB-damaged loci in the yeast genome showed increased mobility and relocation to the nuclear periphery. However, the driving forces behind DSB-induced chromatin dynamics remain unclear. In this study, mathematical models of normal and DSB-damaged yeast chromosomes were developed to simulate their structural dynamics. The effects of histone degradation in the whole nucleus and the change in the physical properties of damaged loci due to the binding of SUMOylated repair proteins were considered in the model of DSB-induced chromosomes based on recent experimental results. The simulation results reproduced DSB-induced changes to structural and dynamical features by which the combination of whole nuclear histone degradation and the rigid structure formation of repair protein accumulations on damaged loci were suggested to be primary contributors to the process by which damaged loci are relocated to the nuclear periphery.

biophysics↗

Epigenetic-structural changes in X chromosomes promote Xic pairing during early differentiation from mouse embryonic stem cells

X chromosome inactivation center (Xic) pairing is robustly observed during the differentiation of embryonic stem (ES) cells from female mouse embryos, and this process is related to X chromosome inactivation, the circadian clock, intra-nucleus architecture, and metabolism. However, the mechanisms underlying the identification and approach of X chromosome pairs in the crowded nucleus are unclear. To elucidate the driving force of Xic pairing, we developed a coarse-grained molecular dynamics model of intranuclear chromosomes in ES cells and in cells 2 days after the onset of differentiation (2-days cells) by considering intrachromosome epigenetic-structural feature-dependent mechanics. The analysis of the experimental data showed X-chromosomes change to specifically softer than autosomes during the cell differentiation by the rearrangement of their distributions of open-close chromatin regions, and the simulations of these models exhibited such softening promoted the mutual approach of the Xic pair. These findings suggested that local intrachromosomal epigenetic features may contribute to the regulation of cell species-dependent differences in intranuclear architecture.

biophysics↗

H+/K+ ion pump enhances cytoskeletal polarity to drive gastrulation in sea urchin embryo

Gastrulation is a universal process in the morphogenesis of many animal embryos. Although morphological and molecular events in gastrulation have been well studied, the mechanical driving forces and underlying regulatory mechanisms are not fully understood. Here, we investigated the gastrulation of embryos of a sea urchin, Hemicentrotus pulcherrimus, which involves the invagination of a single-layered vegetal plate into the blastocoel. We observed that omeprazole, a proton pump inhibitor capable of perturbing the left-right asymmetry of sea urchin embryo, induced "partial exogastrulation" where the secondary invagination proceeds outward. During early gastrulation, intracellular apical-basal polarity of F-actin distribution in vegetal half were higher than those in animal half, while omeprazole treatment disturbed the apical-basal polarity of F-actin distribution in vegetal half. Furthermore, gastrulation stopped and even partial exogastrulation did not occur when F-actin polymerization or degradation in whole embryo was partially inhibited via RhoA or YAP1 knockout. A mathematical model of the early gastrulation reproduced the shapes of both normal and exogastrulating embryos using cell-dependent cytoskeletal features based on F-actin. Additionally, such cell position-dependent intracellular F-actin distributions might be regulated by intracellular pH distributions. Therefore, apical-basal polarity of F-actin distribution disrupted by omeprazole may induce the partial exogastrulation via anomalous secondary invagination.

developmental biology↗

Identification of transcription termination defects at DNA hypomethylated transcription termination sites in DNA methyltransferase 3a-deficient vertebrates.

CpG methylation in genomic DNA is well known as a repressive epigenetic marker in eukaryotic transcription, and DNA methylation of the promoter regions is correlated with silencing of gene expression. In contrast to the promoter regions, the function of DNA methylation during transcription termination remains to be elucidated. A recent study has revealed that mouse DNA methyltransferase 3a (Dnmt3a) mainly functions in de novo methylation in the promoter and gene body regions (including transcription termination sites (TTSs)) during development. To investigate the relationship between DNA methylation overlapping the TTSs and transcription termination, we employed two strategies: informatic analysis using already deposited datasets of Dnmt3a-/- mouse cells and the zebrafish model system. Bioinformatic analysis using methylome and transcriptome data showed that hypomethylated differentially methylated regions overlapping the TTSs were associated with increased read counts and chimeric transcripts downstream of TTSs in Dnmt3a-/- Agouti-related protein neurons, but not in Dnmt3a-/- embryonic stem cells and mouse embryonic fibroblasts. We experimentally detected increased read-through and chimeric transcripts downstream of hypomethylated TTSs in zebrafish maternal-zygotic dnmt3aa-/- mutant. This study is the first to identify transcription termination defects in DNA hypomethylated TTSs in Dnmt3a-/- vertebrates.

genomics↗

Genetically engineered retina for improved retinal reconstruction after transplantation

ES/iPS-retinal sheet transplantation, which supplies photoreceptors as well as other retinal cells, has been shown able to restore visual function in mice with end-stage retinal degeneration. Here, by introducing a novel type of genetically engineered ES/iPS-retinal sheet with reduced numbers of secondary retinal neurons but intact photoreceptor cell layer structure, we reinforced the evidence that ES/iPS-retinal sheet transplantation can establish synaptic connections with the host, restore light responsiveness and reduce aberrant RGC spiking. Furthermore, we show that genetically engineered grafts can substantially improve the outcome of the treatment by improving neural integration. We speculate that this leads to reduced spontaneous activity in the host which in turn contributes to a better visual recovery.

neuroscience↗

The Superior Frontal Longitudinal Tract: Connection between the Dorsal Premotor and the Dorsolateral Prefrontal Cortices

The structural connection between the dorsal premotor (PMd) and the lateral prefrontal cortices (DLPFC) has been revealed, in a few studies, as the frontal longitudinal system (FLS). This study conducted a tractography analysis and a limited, postmortem, white-fiber dissection to investigate the superior FLS tract (SFLT) and analyze both its symmetry and termination point patterns. An analysis of spatial location, termination points, laterality, and correlation with the subjects gender or handedness was performed. SFLT was constructed in 100% of right and 88% of left hemispheres. The tracts exhibited variable patterns in different subjects in their posterior terminations. Additionally, the SFLT was found to possess a complex spatial relationship with the adjacent bundles. The SFLT was revealed successfully in two right hemispheres, where the posterior terminations were found to originate in the PMd, and its posterior terminations being totally separate from the superior longitudinal fasciculus.

neuroscience↗

Affinity of rhodopsin to raft enables the aligned oligomer formation from dimers: Coarse-grained molecular dynamics simulation of disk membranes

The visual photopigment protein rhodopsin (Rh) is a typical G protein-coupled receptor (GPCR) that initiates the phototransduction cascade in retinal disk membrane of rod-photoreceptor cells. Rh molecule has a tendency to form dimer, and the dimer tends to form rows, which is suggested to heighten phototransduction efficiency in single-photon regime. In addition, the dimerization confers Rh an affinity for lipid raft, i.e. raftophilicity. However, the mechanism by which Rh-dimer raftophilicity contributes to the organization of the higher order structure remains unknown. In this study, we performed coarse-grained molecular dynamics simulations of a disk membrane model containing unsaturated lipids, saturated lipids with cholesterol, and Rh-dimers. We described the Rh-dimers by two-dimensional particle populations where the palmitoyl moieties of each Rh exhibits raftophilicity. We simulated the structuring of Rh in a disk for two types of Rh-dimer, i.e., the most and second most stable Rh dimers, which exposes the raftophilic regions at the dimerization-interface (H1/H8 dimer) and two edges away from the interface (H4/H5 dimer), respectively. Our simulations revealed that only the H1/H8 dimer could form a row structure. A small number of raftophilic lipids recruited to and intercalated in a narrow space between H1/H8 dimers stabilize the side-by-side interaction between dimers in a row. Our results implicate that the nano-sized lipid raft domains act as a "glue" to organize the long row structures of Rh-dimers.

biophysics↗

Trans-omic analysis reveals allosteric and gene regulation-axes for altered glucose-responsive liver metabolism associated with obesity

Impaired glucose tolerance associated with obesity causes postprandial hyperglycemia and can lead to type 2 diabetes. To study the differences in liver metabolism in the healthy and obese states, we constructed and analyzed trans-omic glucose-responsive metabolic networks with layers for metabolites, expression data for metabolic enzyme genes, transcription factors, and insulin signaling proteins from the livers of healthy and obese mice. We integrated multi-omic time-course data from wild-type (WT) and leptin-deficient obese (ob/ob) mice after orally administered glucose. In WT mice, metabolic reactions were rapidly regulated (within 10 minutes of oral glucose administration) primarily by glucose-responsive metabolites, especially ATP and NADP+, which functioned as allosteric regulators and substrates of metabolic enzymes, and by Akt-dependent glucose-responsive genes encoding metabolic enzymes. In ob/ob mice, most rapid regulation by glucose-responsive metabolites was absent; instead, glucose administration produced slow changes in the expression of metabolic enzyme-encoding genes to alter metabolic reactions in a time scale of hours. Few common regulatory events occurred in both the healthy and obese mice. Thus, our trans-omic network analysis revealed regulation of liver metabolism in response to glucose is mediated through different mechanisms in the healthy and obese states: Rapid changes in allosteric regulators and substrates and in gene expression dominate the healthy state, and slow transcriptional regulation dominates the obese state.\n\nOne Sentence SummaryRapid changes in regulatory metabolites and gene expression dominate the healthy state, and slow transcriptional regulation dominates the obese state.

systems biology↗

Single-cell information analysis reveals small intra- and large intercellular variations increase cellular information capacity

Cells transmit information about extracellular stimulation through signaling pathways to control cellular function. A signaling pathway can be regarded as a communication channel. In the analysis of channels of cell populations, intercellular variation is considered noise. However, intercellular variation enables individual cells to encode different information. Therefore, at the single-cell level, each cell can be regarded as an independent channel. Thus, we propose that responses of cells of the same type in tissues, such as the fibers in a skeletal muscle, should be regarded as a multiple-cell channel composed of single-cell channels, in which intercellular variation contains information. Here, we applied electrical pulses to individual myotubes from cultured C2C12 cells or dissociated skeletal muscle fibers and measured Ca2+ responses or contraction, respectively, to estimate information capacity in a biological system. For each muscle cell system, we found that a single-cell channel transmitted more information than did a cell-population channel, indicating that the cellular response is consistent with each cell (low intracellular variation) but different among individual cells (high intercellular variation). As cell number and thus the number of single-cell channels increased, a multiple-cell channel transmitted more information by incorporating the differences among individual cells. Thus, a tissue with small intracellular and large intercellular variations has the capacity to distinguish differences in stimulation intensity to precisely control physiological function.\n\nOne Sentence SummarySmall intracellular and large intercellular variations increase information transmission for precise control of tissue function.

systems biology↗

Skull base invasive low-grade meningiomas, a distinct genetic subgroup: A microarray gene expression profile analysis.

IntroductionMeningioma is the most common adult primary brain tumor originating from meningeal coverings of the brain and spinal cord. Commonly, World Health Organization (WHO) grade-I meningiomas are slowly growing and surgically curative, some present with clinically aggressive behavior, invading the skull base bone and soft tissues by extending into the extracranial spaces.\n\nMethodsTo detect the genetic background of the Skull Base Invasive Low-grade Meningioma (SBILM), we conducted a comprehensive analysis of gene expression was conducted on 32 meningioma samples.\n\nResultsThe cluster analysis of the gene expression profile demonstrated a distinctive clustering pattern of the SBILM. Based on the clinical behavior and the microarray findings, they might be a distinct subgroup of meningiomas.\n\nConclusionFurther studies on characterization of genes specifically expressed by the SBILM could lead to the development of diagnostic tools, differentiating it from other WHO grade-I meningiomas and assist in the appropriate management and follow-up strategy, and open the door for development of pharmacological therapies.

genomics↗

Logical design of oral glucose ingestion pattern minimizing blood glucose in humans

Excessive increase in blood glucose level after eating increases the risk of macroangiopathy, and a method for not increasing the postprandial blood glucose level is desired. However, a logical design method of the dietary ingestion pattern controlling the postprandial blood glucose 2 level has not yet been established. We constructed a mathematical model of blood glucose control by oral glucose ingestion in 3 healthy human subjects, used the model to predict an optimal glucose ingestion pattern, and showed that the optimal ingestion pattern minimized the peak value of blood glucose level. Subjects orally ingested 3 doses of glucose by bolus or over 2 hours, and blood glucose, insulin, C-peptide and incretins were measured for 4 hours. We constructed an ordinary differential equation model that reproduced the time course data of the blood glucose and blood hormone levels. Using the model, we predicted that intermittent ingestion 30 minutes apart was the optimal glucose ingestion patterns that minimized the peak value of blood glucose level. We confirmed with subjects that this intermittent pattern decreased the peak value of blood glucose level. This approach could be applied to design optimal dietary ingestion patterns.\n\nIn BriefAs a forward problem, we measured blood glucose and hormones in three human subjects after oral glucose ingestion and constructed a mathematical model of blood glucose control. As an inverse problem, we used the model to predict the optimal oral glucose ingestion pattern that minimized the peak value of blood glucose level, and validated the pattern with the subjects.\n\nHighlightsO_LIModeling blood glucose concentrations predicts an intermittent ingestion pattern is optimal\nC_LIO_LIHuman validation shows ingestion at 30-minute intervals limits peak blood glucose\nC_LIO_LIWe provide a strategy to design optimal dietary ingestion patterns\nC_LI

systems biology↗