Biology subjects

Sakakura, M.

Publications and source records attributed to Sakakura, M..

5 recordsLinked to original sources

bioRxiv2024

Inflammatory molecules in the glomerular endothelium in mild IgA-Nephropathy identified by single-cell and spatial transcriptome

Immunoglobulin A nephropathy (IgA-N) is a primary glomerulonephritis characterized by mesangial cell proliferation and expansion. It still leads to end-stage renal disease over the long course of the disease in many patients. Although glomerular endothelial cells (GE) have been implicated in the pathogenesis of IgA-N, their role remains poorly understood. We conducted single-cell and spatial transcriptomic analysis using human specimens with mild IgA-N compared with normal. We observed the significantly higher expression of several inflammation-associated molecules which have been reported and not reported to be involved in IgA-N pathogenesis, respectively. Furthermore, we show that several important molecules were also highly expressed in GE of IgA-N at protein level by tissue immunostaining. Our analysis suggests that the characteristic pathways identified in GE that involve these molecules are associated with the progression of IgA-N. These findings offer important insights on both the pathogenesis of IgA-N and its treatment at an early stage.

bioinformatics↗

bioRxiv2023

Structural bases for the Charcot-Marie-Tooth disease induced by single amino acid substitutions of myelin protein zero

Myelin protein zero (MPZ or P0) is a major transmembrane protein expressed in peripheral compact myelin and functions to glue membranes to form multiple layered membranes characteristic of myelin. Intermembrane adhesion is mediated by homophilic interactions between the extracellular domains (ECDs) of MPZ molecules. Single amino acid substitutions in an ECD cause demyelinating neuropathy, known as Charcot-Marie-Tooth disease (CMT); however, the mechanisms by which such substitutions induce the disease are not well understood. To address this issue, we constructed a novel assay to evaluate the membrane-stacking activity of ECD using ECD-immobilized nanodiscs. Using this novel "nanomyelin" system, we found that octameric (8-meric) ECDs with a stacked-rings-like configuration are responsible for membrane adhesion. Two inter-ECD interactions, cis and head-to-head, are essential to constituting the 8-mer and, consequently, to gluing the membranes. This result was further reinforced by the observation that the CMT-related N87H substitution at the cis interface abolished membrane-adhesion activity. In contrast, the CMT-related D32G and E68V variants of ECD retained membrane-stacking activity, whereas their thermal stability was reduced compared to that of the WT. Reduced thermal stability may lead to impairment of the long-term stability of ECD and the layered membranes of myelin.

neuroscience↗

bioRxiv2022

Circadian volume changes in hippocampal glia studied by label-free interferometric imaging

Complex brain functions, including learning and memory, arise in part from the modulatory role of astrocytes on neuronal circuits. Functionally, the dentate gyrus (DG) exhibits differences in the acquisition of long-term potentiation (LTP) between day and night. We hypothesize that the dynamic nature of astrocyte morphology plays an important role in the functional circuitry of hippocampal learning and memory, specifically in the DG. Standard microscopy techniques, such as differential interference contrast (DIC), present insufficient contrast for detecting changes in astrocyte structure and function and are unable to inform on the intrinsic structure of the sample in a quantitative manner. Recently, gradient light interference microscopy (GLIM) has been developed to upgrade a DIC microscope with quantitative capabilities such as single-cell dry mass and volume characterization. Here, we present a methodology for combining GLIM and electrophysiology to quantify the astrocyte morphological behavior over the day-night cycle. Colocalized measurements of GLIM and fluorescence allowed us to quantify the dry masses and volumes of hundreds of astrocytes. Our results indicate that, on average, there is a 25% cell volume reduction during the nocturnal cycle. Remarkably, this cell volume change takes place at constant dry mass, which suggests that the volume regulation occurs primarily through aqueous medium exchange with the environment.

neuroscience↗

bioRxiv2021

Label-free imaging of collagen fibers in tissue slices using phase imaging with computational specificity

Evaluating the tissue collagen content in addition to the epithelial morphology has been proven to offer complementary information in histopathology, especially in oncology tumor staging and prediction of survival in cancer patients. One imaging modality widely used for this purpose is second harmonic generation microscopy (SHGM), which reports on the nonlinear susceptibility associated with the collagen fibers. Another method is polarization light microscopy (PLM) combined with picrosirius-red (PSR) tissue staining. However, SHGM requires expensive equipment and provides limited throughput, while PLM and PSR staining are not part of the routine surgical pathology workflow. Here, we utilize phase imaging with computational specificity (PICS) to computationally infer the collagen distribution of unlabeled tissue, with high specificity. PICS utilizes deep learning to translate quantitative phase images (QPI) into corresponding PSR images with high accuracy and inference speed of 200 milisecond per forwardpass through the model once trained. We developed a multimodal imaging instrument that yields both Spatial light Inference Microscopy (SLIM) and polarized light microscopy (PLM) images from the same field of view. Our results indicate that the distributions of collagen fiber orientation, length, and straightness reported by PICS closely match the ones from ground truth as defined by KL-divergence.

pathology↗

bioRxiv2019

Rad51 Interaction Analysis Reveals a Functional Interplay Among Recombination Auxiliary Factors

Although Rad51 is the key protein in homologous recombination (HR), a major DNA double-strand break repair pathway, several auxiliary factors interact with Rad51 to promote productive HR. Here, we present an interdisciplinary characterization of the interaction between Rad51 and Swi5-Sfr1, a widely conserved auxiliary factor. NMR and site-specific crosslinking experiments revealed two distinct sites within the intrinsically disordered N-terminus of Sfr1 that cooperatively bind to Rad51. Although disruption of this binding severely impaired Rad51 stimulation in vitro, interaction mutants did not show any defects in DNA repair. Unexpectedly, in the absence of the Rad51 paralogs Rad55-Rad57, which constitute another auxiliary factor complex, these interaction mutants were unable to promote DNA repair. Our findings provide molecular insights into Rad51 stimulation by Swi5-Sfr1 and suggest that, rather than functioning in an independent subpathway of HR as was previously proposed, Rad55-Rad57 facilitates the recruitment of Swi5-Sfr1 to Rad51.

molecular biology↗