Biology subjects

Chiba, H.

Publications and source records attributed to Chiba, H..

7 recordsLinked to original sources

bioRxiv2026

In vivo xenogenic reconstitution of human alveolar epithelial architecture and function

An urgent need exists for lung models that accurately replicate human physiological profiles. We developed a chimeric mouse model enabling targeted ablation of alveolar type 2 (AT2) cells and lung macrophages, creating niches for endoscopically transplanted human induced pluripotent stem cell (hiPSC)-derived lung progenitors (hLPs). These engrafted cells were retained for 24 weeks, demonstrating self-renewal and differentiation potential, surfactant protein secretion, and maintaining alveolar phosphate homeostasis, suggesting their maturation into AT2 cells. Furthermore, transplantation of hLPs derived from disease-specific hiPSCs recapitulated the phenotype of pulmonary alveolar microlithiasis. The architecture, function, and metabolism of human alveolar epithelium were accurately replicated in vivo. This model has the potential to link experimental models and first-in-human studies, facilitating the development of novel therapies for intractable lung diseases.

developmental biology↗

bioRxiv2025

PAK4 promotes vertex remodeling to maintain epithelial integrity and barrier function

Cell-cell junctions are essential for epithelial integrity and barrier function, but the mechanisms regulating their remodeling remain unclear. Here, we investigated the role of the junctional kinase PAK4 in vertex remodeling. PAK4 localized to apical junctions and accumulated at multicellular vertices in MCDK cells and Xenopus embryos. Inhibition or knockout of PAK4 increased higher-order vertices, caused junctional discontinuities, and impaired barrier function in MDCK cells. PAK4 recruitment required the scaffolding protein Afadin. Afdn-KO cells exhibited severe junctional defects and reduced barrier function. Artificial targeting of PAK4 in Afdn-KO cells partially restored junctional continuity and barrier function. In Xenopus embryos, live imaging showed dynamic PAK4 accumulation at remodeling vertices, and PAK4 inhibition hindered resolution of multicellular vertices. Expression of an amino-terminal fragment (PAK4-NT) impaired remodeling and induced cytokinetic failure. Live imaging in Xenopus revealed barrier leakage at multicellular vertices upon PAK4 inhibition. These findings indicate that PAK4 and Afadin cooperate to maintain epithelial integrity and barrier function by promoting vertex remodeling. SummaryAdhikary et al. show that PAK4, recruited to epithelial junctions by Afadin, drives dynamic vertex remodeling in cells and embryos. Inhibiting PAK4 disrupts tissue packing and compromises junctional continuity and barrier function, implicating PAK4 and Afadin as critical partners in vertex remodeling to preserve tissue integrity.

cell biology↗

bioRxiv2024

Time-course transcriptome data of silk glands in day 0-7 last-instar larvae of Bombyx mori (w1 pnd strain)

Time-course transcriptome expression data were constructed for four parts of the silk gland (anterior, middle, and posterior parts of the middle silk gland, along with the posterior silk gland) in the domestic silkworm, Bombyx mori, from days 0 to 7 of the last-instar larvae. For sample preparation, silk glands were extracted from one female and one male larva every 24 hours accurately after the fourth ecdysis. The reliability of these transcriptome data was confirmed by comparing the transcripts per million (TPM) values of the silk gene and quantitative reverse transcription PCR results. Hierarchical cluster analysis results supported the reliability of transcriptome data. These data are likely to contribute to the progress in molecular biology and genetic research using B. mori, such as elucidating the mechanism underlying the massive production of silk proteins, conducting entomological research using a meta-analysis as a model for lepidopteran insect species, and exploring medical research using B. mori as a model for disease species by utilising transcriptome data.

molecular biology↗

bioRxiv2024

Triterpene RDF: Developing a database of plant enzymes and transcription factors involved in triterpene biosynthesis using the Resource Description Framework

Plants produce structurally diverse triterpenes (triterpenoids and steroids). Their biosynthesis occurs from a common precursor, namely 2,3-oxidosqualene, followed by cyclization catalyzed by oxidosqualene cyclases (OSCs) to yield various triterpene skeletons. Steroids, which are biosynthesized from cycloartenol or lanosterol, are essential primary metabolites in most plant species, along with lineage-specific steroids, such as steroidal glycoalkaloids found in the Solanum species. Other diverse triterpene skeletons are converted into triterpenoids, often classified as specialized compounds that are biosynthesized only in a limited number of plant species with tissue-or cell-type-specific accumulation in plants. Recent studies have identified various tailoring enzymes involved in the structural diversification of triterpenes as well as transcription factors that regulate the expression of these enzymes. However, the coverage of these proteins is scarce in publicly available databases for curated proteins or enzymes, which complicates the functional annotation of newly assembled genomes or transcriptome sequences. Here, we created the Triterpene RDF, a manually curated database of enzymes and transcription factors involved in plant triterpene biosynthesis. The database (https://github.com/ktamura2021/triterpene_rdf/) contains 526 proteins, with links to the UniProt Knowledgebase or NCBI protein database, and it enables direct download of a set of protein sequences filtered by protein type or taxonomy. Triterpene RDF will enhance the functional annotation of enzymes and regulatory elements for triterpene biosynthesis, in a current expansion of availability of genomic information on various plant species.

plant biology↗

bioRxiv2023

Exploring Disease Model Mouse Using Knowledge Graphs: Combining Gene Expression, Orthology, and Disease Datasets

BackgroundThe RIKEN BRC develops and maintains the RIKEN BioResource MetaDatabase to help users explore appropriate target bioresources for their experiments and prepare precise and high-quality data infrastructures. The Swiss Institute of Bioinformatics develops two RDF datasets across multi species for the study of gene expression and orthology: Bgee and Orthologous MAtrix (OMA, an orthology database). MethodsThis study integrates the RIKEN BioResource knowledge graph with Resource Description Framework (RDF) datasets from Bgee, a gene expression database, the OMA, the DisGeNET, a human gene-disease association, Mouse Genome Informatics (MGI), UniProt, and four disease ontologies in the RIKEN BioResource MetaDatabase. Our aim is to explore which model organisms are most appropriate for specific medical science research applications, using SPARQL queries across the integrated datasets. More precisely, we attempt to explore disease-related genes, as well as anatomical parts where these genes are overexpressed and subsequently identify appropriate bioresource candidates available for specific disease research applications. ResultsWe illustrate the above through two use cases targeting either Alzheimers disease or melanoma. We identified two Alzheimers disease-related genes that were overexpressed in the prefrontal cortex (APP and APOE) and 21 RIKEN bioresources predicted to be relevant to Alzheimers disease research. Furthermore, executing a transitive search for the Uberon terms by using the Property Paths function, we identified two melanoma-related genes (HRAS and PTEN), and eight anatomical parts in which these genes were overexpressed, such as the "skin of limb" as an example. Finally, we compared the performance of the federated SPARQL query via the remote Bgee SPARQL endpoint with the performance of a centralized SPARQL query using the Bgee dataset as part of the RIKEN BioResource MetaDatabase. ConclusionsAs a result, we demonstrated that the performance of the federated approach degraded. We concluded that we improved the degradation of the query performance of the federated approach from the BioResource MetaDatabase to the SIB by refining the transferred data through the subquery and enhancing the server specifications, that is optimizing the triple store query evaluation.

bioinformatics↗

bioRxiv2022

Zinc-based Ultrasensitive Microscopic Barrier Assay (ZnUMBA): a live-imaging method for detecting epithelial barrier breaches with spatiotemporal precision

Epithelial barrier function is commonly analyzed using transepithelial electrical resistance (TER), which measures the ion flux across epithelia, or by adding traceable macromolecules to one side of the epithelium and monitoring their passage to the other side. While these methods effectively measure changes to global barrier function, they are not sensitive enough to detect local or transient disruptions in the barrier, and they do not reveal the location of barrier breaches within the context of cell or tissue morphology. Therefore, we developed a method that we named Zinc-based Ultrasensitive Microscopic Barrier Assay (ZnUMBA), which overcomes these limitations, allowing for detection of local tight junction (TJ) leaks with high spatial and temporal resolution (Stephenson et al., 2019; Varadarajan et al., 2021). Here, we present expanded applications for ZnUMBA. First, we show that ZnUMBA can be used in Xenopus embryos to measure the dynamics of barrier restoration and actin dynamics following laser injury of the junction. We also demonstrate that ZnUMBA can be effectively utilized in developing zebrafish embryos as well as cultured monolayers of Madin-Darby Canine Kidney II (MDCK II) epithelial cells. ZnUMBA is a powerful and flexible method that, with some optimization, can be applied to multiple systems to measure dynamic changes in barrier function with spatiotemporal precision.

cell biology↗

bioRxiv2020

Aberrant claudin-6-adhesion signal promotes endometrial cancer progression via estrogen receptor α

Cell adhesion proteins not only maintain tissue integrity but also possess signaling abilities to organize diverse cellular events in physiological and pathological processes; however, the underlying mechanism remains obscure. Among cell adhesion molecules, the claudin (CLDN) family often possesses aberrant expression in various cancers, but the biological relevance and molecular basis have not yet been established. Here, we show that high CLDN6 expression promotes endometrial cancer progression and represents the poor prognostic marker. The second extracellular domain and Y196/200 of CLDN6 were required to recruit and activate Src-family kinases (SFKs) and to stimulate malignant phenotypes. Importantly, we demonstrate that the CLDN6/SFK/PI3K-dependent AKT and SGK (serum- and glucocorticoid-regulated kinase) signalings target Ser518 in the human estrogen receptor and ligand-independently activate target genes in endometrial cancer cells, resulting in cancer development. The identification of this machinery highlights regulation of the transcription factors by cell adhesion to advance tumor progression.

cancer biology↗