Biology subjects

Ishimoto, Y.

Publications and source records attributed to Ishimoto, Y..

6 recordsLinked to original sources

bioRxiv2026

Studies of mice with a large deletion of the ARPKD-associated Pkhd1 locus likely explain its GWAS association with glaucoma in humans

PKHD1, the gene primarily mutated in human autosomal recessive polycystic kidney disease, is one of the top 20 genes associated with primary open angle glaucoma (POAG) and associated endophenotypes in Genome-Wide Association Studies. Here, we show that Pkhd1del3-67/del3-67 mutant mice develop congenital glaucoma due to anterior segment dysgenesis. Using a combination of genetic, epigenetic, bioinformatics and mouse developmental biology approaches, we show that Pkhd1del3-67/del3-67 mice lack Tfap2b and AP-2{beta} expression in a subset of periocular mesenchymal cells at E13.5 and its derivatives. Our data suggest that the Pkhd1del3-67 deletion disrupts features of the Pkhd1-Tfap2b genomic architecture essential for Tfap2b cell-specific activities. Consistent with this model, Pkhd1del3-67/+;Tfap2bko/+trans-heterozygotes lack Tfap2b and AP-2{beta} in relevant cell-types and have similar eye abnormalities as neural crest cell-specific Tfap2bko mutants. These findings provide a likely causal explanation for how SNPs associated with PKHD1 are functionally linked to POAG and add insight into understanding the complexity of disease-causing SNP associations and gene regulatory mechanisms.

genetics↗

bioRxiv2024

Temporal changes in surface tension guide the accurate asymmetric division of Arabidopsis zygotes

In most plants, the zygote divides asymmetrically to define the body axis. In Arabidopsis thaliana, the zygote undergoes polar elongation maintaining a transverse band of cortical microtubules (MTs), and divides asymmetrically forming another MT band, preprophase band (PPB). How the MT band is maintained at the actively growing cell tip and whether it contributes to PPB formation remain elusive. By combining live-cell imaging and mechanical simulation, we show that zygote elongation induces a temporal change (large material derivative) in surface tension at the growing tip to maintain the MT band, which in turn supports polar elongation. The MT band then guides PPB to determine the cell division site. Therefore, autonomous mechanical feedback between cell elongation and MT organization ensures the zygote division asymmetry.

plant biology↗

bioRxiv2024

A viscoelastic-plastic deformation model of hemisphere-like tip growth in Arabidopsis zygotes

Plant zygote cells exhibit tip growth, producing a hemisphere-like tip. To understand how this hemisphere-like tip shape is formed, we revisited a viscoelastic-plastic deformation model that enabled us to simultaneously evaluate the shape, stress, and strain of Arabidopsis (Arabidopsis thaliana) zygote cells undergoing tip growth. Altering the spatial distribution of cell wall extensibility revealed that cosine-type distribution and growth in a normal direction to the surface creates a stable hemisphere-like tip shape. Assuming these as constraints for cell elongation, we determined the best-fitting parameters for turgor pressure and wall extensibility to computationally reconstruct an elongating zygote that retained its hemisphere-like shape using only cell contour data, leading to formulation of non-dimensional growth parameters. Our computational results demonstrate the different morphologies in elongating zygotes through effective non-dimensional parameters.

plant biology↗

bioRxiv2022

PKR activation-induced mitochondrial dysfunction in HIV-transgenic mice with nephropathy

HIV disease remains prevalent in the USA and chronic kidney disease remains a major cause of morbidity in HIV-1-positive patients. Host double-stranded RNA (dsRNA)-activated protein kinase (PKR) is a sensor for viral dsRNA, including HIV-1. We show that PKR inhibition by compound C16 ameliorates the HIV-associated nephropathy (HIVAN) kidney phenotype in the Tg26 transgenic mouse model, with reversal of mitochondrial dysfunction. Combined analysis of single-nucleus RNA-seq and bulk RNA-seq data revealed that oxidative phosphorylation was one of the most downregulated pathways and identified signal transducer and activator of transcription (STAT3) as a potential mediating factor. We identified in Tg26 mice a novel proximal tubular cell cluster enriched in mitochondrial transcripts. Podocytes showed high levels of HIV-1 gene expression and dysregulation of cytoskeleton-related genes; and these cells dedifferentiated. In injured proximal tubules, cell-cell interaction analysis indicated activation of the profibrogenic PKR-STAT3-platelet derived growth factor (PDGF)-D pathway. These findings suggest that PKR inhibition and mitochondrial rescue are potential novel therapeutic approaches for HIVAN. Translational StatementThis work identified mitochondrial dysfunction in transgenic mice manifesting HIV-associated nephropathy mice kidney, using combination of single-nuclear and bulk RNA-seq analysis. Kidney damage was ameliorated by the PKR inhibitor C16, and mitochondrial rescue was shown by transcriptomic profiling and functional assay. These findings suggest that PKR inhibition and mitochondrial rescue are potential therapeutic approaches for HIV-associated nephropathy.

pathology↗

bioRxiv2022

Use of a novel knock-in allele of Pkd1 identifies nicotinamide nucleotide dehydrogenase as a mitochondrial binding partner of polycystin-1

The localization and function of Polycystin-1, the protein encoded by the gene most commonly mutated in autosomal dominant polycystic kidney disease, remains controversial. We have recently reported that its C-terminus is cleaved and traffics to the mitochondria rather than to the nucleus as had been previously described, and we found that absence of PC1 resulted in fragmented mitochondrial networks and increased mitochondrial membrane potential. Direct visualization of PC1 in mitochondria was only possible, however, after over-expression of recombinant, fluorescently labeled-PC1 in a cell culture system. To resolve the issue, we generated a new mouse model with three copies of the HA epitope and eGFP knocked-in frame into the endogenous mouse Pkd1 gene by CRISPR/Cas9. We show that the modified allele is fully functional but the eGFP-tagged protein cannot be detected without antibody amplification methods. We were, however, able to use nanobody-coupled beads and large quantities of tissue to isolate a PC1 interactome and verify nicotinamide nucleotide transhydrogenase (Nnt) as a mitochondrial partner, linking PC1 to regulation of reactive oxygen species levels in the mitochondria. Loss of Nnt function had no significant effect on renal cystic disease in Pkd1 mutants but treatment of young mice with early onset cystic disease with n-acetyl-cysteine (NAC) provided modest benefit only in the Nnt+/+ genetic background. These studies suggest that new methods and brighter tags will be required to track endogenous PC1, but this new mouse model will be a valuable resource for characterizing the protein interactome of endogenous PC1. The data also support our prior findings that the PC1 C-terminus localizes to mitochondria and regulates their function.

genetics↗

bioRxiv2018

Dynamic 3D tissue architecture directs BMP morphogen signaling during Drosophila wing morphogenesis

At the level of organ formation, tissue morphogenesis drives developmental processes in animals, often involving the rearrangement of two-dimensional (2D) structures into more complex three-dimensional (3D) tissues. These processes can be directed by growth factor signaling pathways. However, little is known about how such morphological changes affect the spatiotemporal distribution of growth factor signaling. Here, using the Drosophila pupal wing, we address how Decapentaplegic (Dpp) / Bone Morphogenetic Protein (BMP) signaling and 3D wing morphogenesis are coupled. Dpp, expressed in the longitudinal veins (LVs) of the pupal wing, initially diffuses laterally during the inflation stage to regulate cell proliferation. Dpp localization is then refined to the LVs within each epithelial plane, but with active interplanar signaling for vein patterning, as the two epithelia appose. Our data further suggest that the 3D architecture of the wing epithelia directs the spatial distribution of BMP signaling, revealing how 3D morphogenesis is an emergent property of the interactions between extracellular signaling and tissue shape changes.

developmental biology↗