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Furuta, Y.

Publications and source records attributed to Furuta, Y..

14 recordsLinked to original sources

Genetically engineered ESC-derived embryos reveal Vinculin-dependent force responses required for mammalian neural tube closure

Epithelial sheets build complex structures by converting mechanical forces into changes in cell and tissue organization. During neural tube closure, the neural plate dynamically remodels to produce a closed tube that provides the structural foundation for the developing brain and spinal cord. How cells maintain epithelial integrity despite the forces required for tissue morphogenesis during neural tube closure is not understood. We show that mechanical forces are upregulated during cranial neural tube closure in the mouse embryo and recruit the force-sensitive protein Vinculin to adherens junctions. Leveraging a genetically engineered embryonic stem cell-based pipeline to efficiently generate mutant embryos, we show that Vinculin mutants produce mechanical forces correctly but fail to maintain cell adhesion under tension, resulting in a failure of cranial neural fold elevation. Live imaging of cell behavior in the developing midbrain reveals that apical constriction, cell rearrangement, and cell division initiate correctly in Vinculin mutants, but their progression is impeded by disruption of adherens junctions at sites of increased tension. These results demonstrate that Vinculin is required to reinforce cell adhesion in response to increasing physiological forces during cranial neural tube closure, and that this activity is necessary to translate these forces into changes in tissue structure.

developmental biology↗

Noninvasive reconstruction of complete mitochondrial genomes from aquatic environmental DNA using PCR-free long-read sequencing

O_LIEnvironmental DNA (eDNA) is a powerful, noninvasive data source for assessing aquatic biodiversity, but the assumption that it is present only in low concentrations and highly fragmented forms has limited its use. Accordingly, eDNA genomic analyses have focused on short mitochondrial regions, which often lack the resolution for accurate species identification or individual-level analysis. However, some intact mitochondrial genomes may persist in aquatic environments, and their recovery could enable noninvasive determination of complete mitochondrial sequences, providing higher-resolution genetic information. Nevertheless, most eDNA studies have overlooked long-read DNA analysis, and current protocols are not optimised to detect or utilise these longer fragments. C_LIO_LITo address this, we developed a long-read sequencing workflow to reconstruct complete mitochondrial genomes from eDNA. First, we selected the optimal DNA extraction method and filter pore sizes using water from aquaria containing Carassius auratus or Oryzias latipes, aiming to maximise the yield of high-molecular-weight DNA for target organism sequences. We then applied two sequencing strategies: a PCR-free approach using native eDNA and a long-range PCR-based approach targeting the complete mitochondrial genome. C_LIO_LIUsing the determined DNA extraction method and a filter (1.2 {micro}m pore size), we obtained high-molecular-weight DNA suitable for long-read sequencing. In the PCR-free approach, C. auratus samples from single-fish aquaria yielded hundreds of reads mapped to the mitochondrial genome, with some reads exceeding 16,000 bp. These allowed de novo assembly of full-length mitochondrial genomes in several samples. In the PCR-based approach, one sample yielded over 100,000 mitochondrial reads, of which >27% exceeded 16,000 bp, enabling assemblies. Comparison with assemblies from tissue-derived DNA confirmed accuracy, as sequences were nearly identical. Across samples, polymorphism analysis revealed two distinct haplotypes in C. auratus. These results demonstrate that full-length mitochondrial genomes can be reconstructed from eDNA, and that both PCR-free and PCR-based strategies are effective under appropriate sample conditions. C_LIO_LIOur results show that long-read sequencing enables the recovery of near-complete mitochondrial genomes directly from eDNA without requiring artificial fragmentation and, in some cases, without the need for enrichment steps. This approach enhances eDNA-based biodiversity monitoring by improving species identification and enabling within-population level analyses. C_LI

ecology↗

Engineered coagulation factor VIII with enhanced secretion and coagulation potential for hemophilia A gene therapy

The major challenges of gene therapy for hemophilia A using adeno-associated virus (AAV) vectors are reducing vector doses and the long-term maintenance of stable factor VIII (FVIII). Here, we developed engineered human B-domain-deleted FVIIIs (FVIIISQs) with enhanced secretion and coagulation potential. Intracellular accumulation was markedly reduced in some engineered FVIIISQs, resulting in reduced unfolded protein responses. The administration of AAV vectors carrying engineered FVIIISQ to hemophilia A mice resulted in approximately eight-fold higher FVIII activity and four-fold higher FVIII antigen levels compared with wild-type FVIIISQ administration. The specific FVIII activity of the engineered FVIIISQ was 3.6 times higher than that of the wild-type FVIIISQ, and its binding to activated coagulation factor IX was significantly enhanced, which is supported by the structural analysis. In macaques, the administration of AAV5 vector carrying the engineered FVIIISQ without CpG sequences resulted in a supra-physiological increase in plasma FVIII activity at a dose one-thirtieth that of valoctocogene roxaparvovec (2 x 1012 vg/kg). The engineered FVIIISQ may thus provide stable, long-term therapeutic efficacy in AAV-mediated hemophilia A gene therapy even at low doses.

bioengineering↗

A ground surface rolling method for detecting environmental DNA of terrestrial animals

Biological information obtained from environmental DNA has been helpful for conservation of ecosystems and biodiversity. Methods for environmental DNA of terrestrial habitats are limited such as sampling of water near terrestrial habitat and of shoveled soil, whereas those of aquatic habitats are well-established. We developed a method using a sampler for terrestrial habitat utilizing a combination of a simple rotating body and a single-use non-woven fabric collector as a sampler, enabling sample collection from wide area of various surfaces without power supply. The sampler was applied to collect 90 ground surface and 29 water samples in a secondary nature environment, resulted in the detection of 53 species of birds and mammals in total. The result covered 92% of the species detected by cameras installed in front of the sampling areas, validating the sensitivity of the method. Time course analysis also revealed that the timing of the detection of birds matched that of the birds actual arrival. These results suggest that our labor-saving method could provide accurate and time-resolved data for biodiversity monitoring of terrestrial areas. Combining with established aquatic environmental analysis, the sampler would enable systematic monitoring of both aquatic and terrestrial habitats, enhancing our understanding of the whole ecosystem.

ecology↗

Genetic variation modulates susceptibility to aberrant DNA hypomethylation and imprint deregulation in naive pluripotent stem cells

Naive pluripotent stem cells (nPSC) frequently undergo pathological and not readily reversible loss of DNA methylation marks at imprinted gene loci. This abnormality poses a hurdle for using pluripotent cell lines in biomedical applications and underscores the need to identify the causes of imprint instability in these cells. We show that nPSCs from inbred mouse strains exhibit pronounced strain-specific susceptibility to locus-specific deregulation of imprinting marks during reprogramming to pluripotency and upon culture with MAP kinase inhibitors, a common approach to maintain naive pluripotency. Analysis of genetically highly diverse nPSCs from the Diversity Outbred (DO) stock confirms that genetic variation is a major determinant of epigenome stability in pluripotent cells. We leverage the variable DNA hypomethylation in DO lines to identify several trans-acting quantitative trait loci (QTLs) that determine epigenome stability at either specific target loci or genome-wide. Candidate factors encoded by two multi-target QTLs on chromosomes 4 and 17 suggest specific transcriptional regulators that contribute to DNA methylation maintenance in nPSCs. We propose that genetic variants represent candidate biomarkers to identify pluripotent cell lines with desirable properties and might serve as entry points for the targeted engineering of nPSCs with stable epigenomes. HighlightsO_LINaive pluripotent stem cells from distinct inbred mouse strains exhibit variable DNA methylation levels at imprinted gene loci. C_LIO_LIThe vulnerability of pluripotent stem cells to loss of genomic imprinting caused by MAP kinase inhibition strongly differs between inbred mouse strains. C_LIO_LIGenetically diverse pluripotent stem cell lines from Diversity Outbred mouse stock allow the identification of quantitative trait loci controlling DNA methylation stability. C_LIO_LIGenetic variants may serve as biomarkers to identify naive pluripotent stem cell lines that are epigenetically stable in specific culture conditions. C_LI

developmental biology↗

A pluripotent stem cell platform for in vitro systems genetics studies of mouse development

The directed differentiation of pluripotent stem cells (PSCs) from panels of genetically diverse individuals is emerging as a powerful experimental system for characterizing the impact of natural genetic variation on developing cell types and tissues. Here, we establish new PSC lines and experimental approaches for modeling embryonic development in a genetically diverse, outbred mouse stock (Diversity Outbred mice). We show that a range of inbred and outbred PSC lines can be stably maintained in the primed pluripotent state (epiblast stem cells -- EpiSCs) and establish the contribution of genetic variation to phenotypic differences in gene regulation and directed differentiation. Using pooled in vitro fertilization, we generate and characterize a genetic reference panel of Diversity Outbred PSCs (n = 230). Finally, we demonstrate the feasibility of pooled culture of Diversity Outbred EpiSCs as "cell villages", which can facilitate the differentiation of large numbers of EpiSC lines for forward genetic screens. These data can complement and inform similar efforts within the stem cell biology and human genetics communities to model the impact of natural genetic variation on phenotypic variation and disease-risk.

developmental biology↗

A stress sensor IRE1α is required for bacterial exotoxin-induced inflammasome activation in tissue-resident macrophages

Cholera toxin (CT), a bacterial exotoxin composed of one A subunit (CTA) and five B subunits (CTB), functions as an immune adjuvant. CTB can induce production of interleukin-1{beta} (IL-1{beta}), a proinflammatory cytokine, in synergy with a lipopolysaccharide (LPS), from resident peritoneal macrophages (RPMs) through the pyrin and NLRP3 inflammasomes. However, how CTB or CT activates these inflammasomes in the macrophages has been unclear. Here, we clarified the roles of IRE1, an endoplasmic reticulum (ER) stress sensor, in CT-induced IL-1{beta} production from RPMs. In RPMs, CTB is incorporated into ER and induced ER stress responses, depending on GM1, a cell membrane ganglioside. IRE1-deficient RPMs showed a significant impairment of CT- or CTB-induced IL-1{beta} production, indicating that IRE1 was required for CT- or CTB-induced IL-1{beta} production from RPMs. This study first demonstrates the critical roles of IRE1 in activation of both NLRP3 and pyrin inflammasomes in tissue-resident macrophages. One sentence summaryIRE1 is required for NLRP3 and pyrin-mediated IL-1{beta} production

immunology↗

Identification, expression, and purification of DNA cytosine 5-methyltransferases with short recognition sequences

BackgroundDNA methyltransferases (MTases) are enzymes that induce methylation, one of the representative epigenetic modifications of DNA, and are also useful tools for analyzing epigenomes. However, regarding DNA cytosine 5-methylation, MTases identified so far have drawbacks in that their recognition sequences overlap with those for intrinsic DNA methylation in mammalian cells and/or that the recognition sequence is too long for fine epigenetic mapping. To identify MTases with short recognition sequences that never overlap with the CG dinucleotide, we systematically investigated the 25 candidate enzymes identified using a database search, which showed high similarity to known cytosine 5-MTases recognizing short sequences. ResultsWe identified MTases with six new recognition sequences, including TCTG, CC, CNG, TCG, GCY, and GGCA. Because the recognition sequence never overlapped with the CG dinucleotide, MTases recognizing the CC dinucleotide were promising. ConclusionsIn the current study, we established a procedure for producing active CC-methylating MTases and applied it to nucleosome occupancy and methylome sequencing to prove the usefulness of the enzyme for fine epigenetic mapping. MTases that never overlap with CG dinucleotides would allow us to profile multiple epigenomes simultaneously.

biochemistry↗

Silkworm model for Bacillus anthracis infection and virulence determination

Bacillus anthracis is an obligate pathogen and a causative agent of anthrax. Its major virulence factors are plasmid-coded; however, recent studies have revealed chromosome-encoded virulence factors, indicating that the current understanding of its virulence mechanism is elusive and needs further investigation. In this study, we established a silkworm (Bombyx mori) infection model of B. anthracis Sterne. We showed that silkworms were killed by B. anthracis and cured of the infection when administered with antibiotics. We quantitatively determined the lethal dose of the bacteria that kills 50% larvae and effective doses of antibiotics that cure 50% infected larvae. Furthermore, we demonstrated that B. anthracis mutants with disruption in virulence genes such as pagA, lef, and atxA had attenuated silkworm-killing ability and reduced colonization in silkworm hemolymph. The silkworm infection model established in this study can be utilized in large-scale infection experiments to identify novel virulence determinants and develop novel therapeutic options against B. anthracis infections.

microbiology↗

Calcium ions trigger the exposure of phosphatidylserine on the surface of necrotic cells

Intracellular Ca2+ level is under strict regulation through calcium channels and intracellular Ca2+ storage pools such as the endoplasmic reticulum (ER). Mutations in certain ion channel subunits, which result in the mis-regulation of Ca2+ influx, cause the excitotoxic necrosis of neurons. In the nematode Caenorhabditis elegans, six mechanosensory (touch) neurons are induced to undergo excitotoxic necrosis by dominant mutations in the DEG/ENaC sodium channel subunits. These necrotic neurons are subsequently engulfed and degraded by neighboring hypodermal cells. We previously reported that the necrotic touch neurons actively expose phosphatidylserine (PS), an "eat-me" signal, to attract engulfing cells. However, the upstream signal that triggers PS externalization remained elusive. Here we report that a robust and transient increase of cytoplasmic Ca2+ level occurs prior to the exposure of PS on the surfaces of necrotic neurons. We further found that inhibiting the release of Ca2+ from the ER, either pharmacologically or genetically through mutations in the gene encoding calreticulin, the ER Ca2+ chaperon, impairs PS exposure on necrotic neurons. On the contrary, inhibiting the re-uptake of cytoplasmic Ca2+ into the ER induces ectopic necrosis and PS exposure. These findings indicate that high levels of cytoplasmic Ca2+ is necessary and sufficient for PS exposure. Remarkably, we found that PS exposure occurred independently of other necrosis events. On the other hand, apoptotic cells, unlike necrotic cells, do not depend on the ER Ca2+ pool for PS exposure. Our findings reveal a necrotic neuron-specific, "two-step Ca2+-influx" pathway that promotes PS exposure on cell surfaces. This pathway is initiated by the modest influx of Ca2+ from the extracellular space and further boosted by the release of Ca2+ from the ER into the cytoplasm. Author SummaryNecrosis is a type of cell death that exhibits distinct morphological features such as cell swelling. Many environmental insults induce cells to undergo necrosis. Necrotic cells expose phosphatidylserine (PS) - a type of phospholipid - on their outer surfaces. Receptor molecules on phagocytes detect phosphatidylserine on necrotic cells and subsequently initiate the engulfment process. As necrosis is associated with stroke, cancer, neurodegenerative diseases, heart diseases, and inflammatory diseases, studying necrotic cell clearance has important medical relevance. In the model organism the nematode C. elegans, by utilizing dominant mutations in ion channels that induce neurons to undergo necrosis, we previously identified membrane proteins that promote the exposure of phosphatidylserine on necrotic cell surfaces. Here, using the same experimental system, we further discover that the necrosis insults trigger an increase of the cytoplasmic Ca2+ level, which in turn promotes PS externalization in necrotic cells. Furthermore, we find that the Ca2+ pool in the endoplasmic reticulum is necessary for the rapid increase of cytoplasmic Ca2+ that helps initiate necrosis. This Ca2+-regulated event is not observed when cells undergoing apoptosis (a form of cell suicide) expose PS. Our findings reveal a novel upstream regulatory mechanism that promotes necrotic cell clearance in animals.

cell biology↗

CDK1 dependent phosphorylation of hTERT contributes to cancer progression

The telomerase reverse transcriptase is upregulated in the majority of human cancers and contributes directly to cell transformation. Here we report that hTERT is phosphorylated at threonine 249 during mitosis by the serine/threonine kinase CDK1. Clinicopathological analyses revealed that phosphorylation of hTERT at threonine 249 occurs more frequently in advanced cancers. Using CRISPR/Cas9 genome editing, we introduced substitution mutations at threonine 249 in the endogenous hTERT locus and found that phosphorylation of threonine 249 is necessary for hTERT-mediated RNA dependent RNA polymerase (RdRP) activity but dispensable for reverse transcriptase activity. Cap Analysis of Gene Expression (CAGE) demonstrated that hTERT phosphorylation at 249 regulates the expression of specific genes that are necessary for cancer cell proliferation and tumor formation. These observations indicate that phosphorylation at threonine 249 regulates hTERT RdRP and contributes to cancer progression in a telomerase independent manner.

cancer biology↗

Therapeutic effects of favipiravir against severe fever with thrombocytopenia syndrome virus infection in a lethal mouse model: dose-efficacy studies upon oral administration

BackgroundSevere fever with thrombocytopenia syndrome (SFTS), caused by SFTS virus (SFTSV), is a viral hemorrhagic fever with a high case fatality rate. Favipiravir was reported to be effective in the treatment of SFTSV infection in vivo in type I interferon receptor knockout (IFNAR-/-) mice at treatment dosages of both 60 mg/kg/day and 300 mg/kg/day for a duration of 5 days.\n\nMethodsIn this study, the efficacy of favipiravir at dosages of 120 mg/kg/day and 200 mg/kg/day against SFTSV infection in an IFNAR-/- mouse infection model was investigated. IFNAR-/- mice were subcutaneously infected with SFTSV at a 1.0 x 106 50% tissue culture infectious dose followed by twice daily administration of favipiravir, comprising a total dose of either 120 mg/kg/day or 200 mg/kg/day. The treatment was initiated either immediately post infection or at predesignated time points post infection.\n\nResultsAll mice treated with favipiravir at dosages of 120 mg/kg/day or 200 mg/kg/day survived when the treatment was initiated at no later than 4 days post infection. A decrease in body weight of mice was observed when the treatment was initiated at 3-4 days post infection. Furthermore, all control mice died. The body weight of mice did not decrease when treatment with favipiravir was initiated immediately post infection at dosages of 120 mg/kg/day and 200 mg/kg/day.\n\nConclusionsSimilar to the literature-reported peritoneal administration of favipiravir at 300 mg/kg/day, the oral administration of favipiravir at dosages of 120 mg/kg/day and 200 mg/kg/day to IFNAR-/- mice infected with SFTSV was effective.\n\nAuthor summarySevere fever with thrombocytopenia syndrome (SFTS), which is caused by SFTS virus (SFTSV), is a generalized infectious disease with a high case fatality rate. Currently, no effective therapeutics for SFTS is available; therefore, the development of effective antiviral drugs is needed. Favipiravir exhibits antiviral activity against various RNA viruses, including SFTSV. The present study demonstrated the efficacy of favipiravir in the treatment of SFTSV infection in a lethal mouse model, when the dose was set similar to that approved for anti-influenza drug in humans by the Ministry of Health, Labour and Welfare, Japan. The present study suggests that favipiravir is a promising drug for the treatment of SFTSV infection.

microbiology↗

Hair Follicle Epidermal Stem Cells Define a Niche for Tactile Sensation

The heterogeneity and compartmentalization of stem cells is a common principle in many epithelia, and is known to function in epithelial maintenance, but its other physiological roles remain elusive. Here we show transcriptional and anatomical contributions of compartmentalized epidermal stem cells (EpSCs) in tactile sensory unit formation in the hair follicle (HF). EpSCs in the follicle upper-bulge, where mechanosensory lanceolate complexes (LCs) innervate, express a unique set of extracellular matrix (ECM) and neurogenesis-related genes. These EpSCs deposit an ECM protein EGFL6 into the collar matrix, a novel ECM that tightly ensheathes LCs. EGFL6 is required for the proper patterning, touch responses, and v integrin-enrichment of LCs. By maintaining a quiescent original EpSC niche, the old bulge, EpSCs provide anatomically stable HF-LC interfaces, irrespective of the stage of follicle regeneration cycle. Thus, compartmentalized EpSCs provide a niche linking the HF and the nervous system throughout the hair cycle.

developmental biology↗

Cell Type Specific Survey of Epigenetic Modifications by Tandem Chromatin Immunoprecipitation Sequencing

BackgroundThe nervous system of higher eukaryotes is composed of numerous types of neurons and glia that together orchestrate complex neuronal responses. However, this complex pool of cells typically poses analytical challenges in investigating gene expression profiles and their epigenetic basis for specific cell types. Here, we developed a novel method that enables cell type-specific analyses of epigenetic modifications using tandem chromatin immunoprecipitation sequencing (tChIP-Seq).\n\nResultsFLAG-tagged histone H2B, a constitutive chromatin component, was first expressed in Camk2a-positive pyramidal cortical neurons and used to purify chromatin in a cell type-specific manner. Subsequent chromatin immunoprecipitation using antibodies against H3K4me3--an active promoter mark--allowed us to survey neuron-specific coding and non-coding transcripts. Indeed, tChIP-Seq identified hundreds of genes associated with neuronal functions and genes with unknown functions expressed in cortical neurons.\n\nConclusionstChIP-Seq thus provides a versatile approach to investigating the epigenetic modifications of particular cell types in vivo.

molecular biology↗