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Sakamoto, N.

Publications and source records attributed to Sakamoto, N..

14 recordsLinked to original sources

Numerical study of spatial and temporal dynamics of integrin clustering during early cell adhesion

Integrins are adhesion proteins that diffuse along the cell membrane, bind to ligands, and cluster with each other in the early stage of cell adhesion. Integrin clustering and its specific spatial distribution play important roles in subsequent biological processes; however, the mechanisms that give rise to their characteristic spatial distribution remain poorly understood. To address this issue, we developed a cell adhesion model that incorporates cell membrane deformation and integrin dynamics. A hybrid continuous/discrete model was applied to represent membrane deformation, whereas Brownian dynamics combined with a transition state model was used to describe integrin dynamics and binding kinetics. Comparison of numerical simulations of cell adhesion to a substrate with experimental observations at the early stage of adhesion successfully reproduced the characteristic spatial distribution of integrin clusters, in which high-density clusters formed at the periphery of the region adhering to the substrate. These results suggest that the cellular-scale distribution of integrin clusters can be reproduced using only minimal elements, such as adhesion-driven membrane deformation and integrin-ligand binding. In addition, we found that the strength of integrin-ligand binding regulates the degree of clustering by changing the size of the part of the membrane that is deformed, thereby mechanically supporting the mechanical involvement of the actin cytoskeleton in integrin clustering. Furthermore, the formation and spatial distribution of integrin clusters were shown to be determined not only by the static mechanical equilibrium of membrane deformation and physical adsorption, but also by membrane spreading/deformation and the dynamic behavior of integrins. This suggests that the size and spatial distribution of integrin clusters may be controllable by modulating the speed of membrane spreading.

biophysics↗

Transcriptomic response to histone deacetylase inhibitors in cultured feline cells

ObjectiveIn recent years, the number of cats kept as companion animals has increased, leading to a growing demand for veterinary care. Although some histone deacetylase (HDAC) inhibitors are promising for the treatment of human cancers and neurological diseases, comprehensive systematic research on HDAC inhibitors in domestic cats remains insufficient. Therefore, this study aimed to investigate the effects of HDAC inhibitors on the transcriptome of feline cells. MethodsTwo types of cells derived from domestic cats, Crandell-Rees Feline Kidney (CRFK; kidney-derived) cells and PG-4 cells (astrocyte-derived), were treated with four HDAC inhibitors (panobinostat, trichostatin A, valproic acid, and vorinostat) for 24 h. Transcriptomic changes after treatment were examined using RNA sequencing. ResultsHDAC inhibitor treatment upregulated the expression of intercellular chemical interactions and signal transduction-related genes, similar to observations in human cells. Although HDAC inhibitors did not suppress the expression of cell cycle-related genes in CRFK cells, as observed in human cells, the inhibitors downregulated the expression of organogenesis-related genes. Consistent with observations in human cells, HDAC inhibitors suppressed the expression of cell cycle- and cancer-related genes in PG-4 cells. Importantly, valproic acid, which is thought to be more effective for neurological diseases than for cancer, suppressed the expression of more cancer-related genes in PG-4 cells than the other three HDAC inhibitors. Conclusion and relevanceOur findings revealed that the responses of cells derived from feline organs to various HDAC inhibitors varied considerably depending on the organ of origin and species. Since few studies, including human studies, have comprehensively compared transcriptomic responses to multiple HDAC inhibitor classes across multiple cell types, the results of this study provide a foundation for future research on the treatment and prevention of cancer and neurological diseases in domestic cats and other mammals.

cell biology↗

Co-targeting an AMPK--MAPK axis reprograms CAFs and suppresses PDAC

Pancreatic ductal adenocarcinoma (PDAC) is a fatal cancer characterized by limited therapeutic options and a highly treatment-resistant tumor microenvironment. Beyond tumor-intrinsic genetic alterations, growing evidence indicates that host-microbiome interactions influence cancer progression through microbial metabolites. However, how microbiome-derived metabolites influence oncogenic signaling in PDAC remains unclear. Here, integrated profiling revealed a consistent reduction of the microbial metabolite acetic acid in fecal samples from treatment-naive patients with PDAC and in a genetically defined Drosophila model recapitulating key PDAC driver alterations. Acetic acid activates AMP-activated protein kinase, and pharmacological activation of this pathway together with inhibition of mitogen-activated protein kinase signaling suppressed tumor growth in fly and mouse models. Combined pathway targeting restored AMPK activity and suppressed cancer-associated fibroblast activation. These findings identify a microbiome-associated metabolic vulnerability in PDAC and suggest that coordinated targeting of metabolic and oncogenic signaling may restrain tumor progression and improve therapeutic strategies.

cancer biology↗

Whole-genome sequencing of CRFK and PG-4 cells to infer the phenotype of the original donors

BackgroundCrandell-Rees Feline Kidney (CRFK; kidney-derived) cells and PG-4 cells (astrocyte-derived) have been in use and have been passaged for decades in laboratories worldwide; however, no detailed information on the genetic background of the donor individuals is available, particularly regarding phenotype characteristics such as coat and iris color. ResultsWe performed whole-genome sequencing of CRFK and PG-4 cells. We analyzed the resulting data to infer the phenotype of the individual from which the cells were derived, specifically for the coat color, coat length, coat pattern, and iris color. Our data suggested that CRFK cells originated from a cat with long black fur lacking stripes and with non-blue irises; PG-4 cells originated from a cat with long bicolored white and black fur without stripes, and with non-blue irises. Analysis of publicly available RNA-seq data confirmed that genes associated with coat phenotype and iris color are expressed in the skin and eyes, as well as in various other organs. ConclusionsVariants of the genes affecting coat phenotype and iris color may influence physiological functions throughout the body. These results shed light on the previously unknown genetic background of commonly used feline cultured cells and the phenotype of the donor individuals. These findings may facilitate more accurate interpretation of data obtained from cultured feline cells and provide guidelines for developing cell lines with domestic cat genotypes exhibiting diverse phenotypes through genome editing. This will help to provide clarity regarding deafness in cats with white fur and blue irises and elucidate the effects of melanocyte destruction caused by KIT gene mutations on the nervous system and the influence of other coat-related factors in organs other than the skin or functions independent of coat formation.

genomics↗

Common tissue-specific expressions and regulatory mechanisms of c-KIT isoforms with and without GNNK and GNSK sequences across five mammals

c-KIT is a transmembrane receptor tyrosine kinase involved in various signaling pathways. Alternative pre-mRNA splicing of KIT results in isoforms that differ in the presence or absence of four amino acid sequences in the extracellular juxtamembrane region, such as, isoforms with and without the GNNK sequence (GNNK+ and GNNK-, respectively) in humans and mice, and those with and without GNSK (GNSK+ and GNSK-, respectively) in domestic dogs, cats, and sheep. These isoforms have been extensively studied as disease-associated (particularly tumors or cancer) splice variants with differing kinase activities. However, the expression patterns and regulatory factors of each isoform in various animal species without tumors or cancer remain poorly understood. Studying these aspects can provide the basis for understanding the associations between c-KIT isoforms and disease. Therefore, in the present study, a comprehensive expression analysis of c-KIT isoforms was conducted using tissue-wide transcriptome data from humans, mice, dogs, cats, and sheep. We found that the expression ratio of c-KIT isoforms differs across tissues, and such features are conserved across animal species: GNNK+ and GNSK+ isoforms have high expression ratios in the central nervous system, while GNNK- and GNSK- predominate in other tissues. Furthermore, NOVA2, RBFOX1, RBFOX3, and DYRK1A were suggested to be candidate factors regulating the selection of the alternative 5' splice donor site of KIT.

bioinformatics↗

MS2Lipid: a lipid subclass prediction program using machine learning and curated tandem mass spectral data

Untargeted lipidomics using collision-induced dissociation-based tandem mass spectrometry (CID-MS/MS) is essential for biological and clinical applications. However, annotation confidence is still guaranteed by manual curation by analytical chemists, although various software tools have been developed for automatic spectral processing based on rule-based fragment annotations. In this study, we provide a novel machine learning model, MS2Lipid, for the prediction of lipid subclasses from MS/MS queries to provide an orthogonal decision of lipidomics software programs to determine the lipid subclass of ion features, in which a new descriptor, MCH (mode of carbon and hydrogen), was designed to increase the specificity of lipid subclasses in nominal mass resolution MS data. The model trained with 5,224 and 5,408 manually curated MS/MS spectra for the positive- and negative-ion modes mapped the query into one or several categories of 97 lipid subclasses, with an accuracy of 95.5% queries in the test set. Our program outperformed the CANOPUS ontology prediction program, providing correct annotations for 38.7% of the same test set. The program was further validated using various datasets from different machines and curators, and the average accuracy exceeded 87.4 %. Furthermore, the function of MS2Lipid was showcased by the annotation of novel esterified bile acids, whose abundance was significantly increased in obese patients in a human cohort study, suggesting that the machine learning model provides an independent criterion for lipid subclass classification, in addition to an environment for annotating lipid metabolites that have been previously unknown.

bioinformatics↗

MS-DIAL 5 multimodal mass spectrometry data mining unveils lipidome complexities

Lipidomics and metabolomics communities comprise various informatics tools; however, software programs that can handle multimodal mass spectrometry (MS) data with structural annotations guided by the Lipidomics Standards Initiative are limited. Here, we provide MS-DIAL 5 to facilitate the in-depth structural elucidation of lipids through electron-activated dissociation (EAD)-based tandem MS, as well as determine their molecular localization through MS imaging (MSI) data using a species/tissue-specific lipidome database containing the predicted collision-cross section (CCS) values. With the optimized EAD settings using 14 eV kinetic energy conditions, the program correctly delineated the lipid structures based on EAD-MS/MS data from 96.4% of authentic standards. Our workflow was showcased by annotating the sn- and double-bond positions of eye-specific phosphatidylcholine molecules containing very-long-chain polyunsaturated fatty acids (VLC-PUFAs), characterized as PC n-3-VLC-PUFA/FA. Using MSI data from the eye and HeLa cells supplemented with n-3-VLC-PUFA, we identified glycerol 3-phosphate (G3P) acyltransferase (GPAT) as an enzyme candidate responsible for incorporating n-3 VLC-PUFAs into the sn-1 position of phospholipids in mammalian cells, which was confirmed using recombinant proteins in a cell-free system. Therefore, the MS-DIAL 5 environment, combined with optimized MS data acquisition methods, facilitates a better understanding of lipid structures and their localization, offering novel insights into lipid biology.

bioinformatics↗

Assembly of continuous high-resolution draft genome sequence of Hemicentrotus pulcherrimus using long-read sequencing

The update of the draft genome assembly of sea urchin, Hemicentrotus pulcherrimus, which is widely studied in East Asia as a model organism of early development, was performed using Oxford nanopore long-read sequencing. The updated assembly provided [~]600 Mb genome sequences divided into 2,163 contigs with N50 = 516 kb. BUSCO completeness score and transcriptome model mapping ratio (TMMR) of the present assembly were obtained as 96.5 % and 77.8 % respectively. These results were more continuous with higher resolution than those by the previous version of H. pulcerrimus draft genome, HpulGenome_v1, where the number of scaffolds = 16,251 with a total of [~]100 Mb gaps, N50 = 143 kb, BUSCO completeness score = 86.1 %, and TMMR = 40.61. The obtained genome contained 36,055 gene models that were consistent with those in other echinoderms. Additionally, two tandem repeat sequences of early histone gene locus containing 47 copies and 34 copies of all histone genes, and 185 of the homologous sequences of the interspecifically conserved region of the Ars insulator, ArsInsC, were obtained. These results provide further advance for genome-wide research of development, gene regulation, and intranuclear structural dynamics of multicellular organisms using Hemicentrotus pulcherrimus.

genomics↗

Skin coat color-dependent risks and risk factors of squamous cell carcinoma and deafness of domestic cats inferred via RNA-seq data

The transcriptome data of skin cells from domestic cats with brown, orange, and white coats were analyzed using a public database to investigate the possible relationship between coat color-related gene expression and squamous cell carcinoma risk, as well as the mechanism of deafness in white cats. We found that the ratio of the expression level of genes suppressing squamous cell carcinoma to that of genes promoting squamous cell carcinoma might be considerably lower than the theoretical estimation in skin cells with orange and white coats in white-spotted cat. We also found the possibility of the frequent production of KIT lacking the first exon (d1KIT) in skin cells with white coats, and d1KIT production exhibited a substantial negative correlation with the expression of SOX10, which is essential for melanocyte formation and adjustment of hearing function. Additionally, the production of d1KIT was expected to be due to the insulating activity of the feline endogenous retrovirus 1 (FERV1) LTR in the 1st intron of KIT and its CTCF binding sequence repeat. These results contribute to basic veterinary research to understand the relationship between cat skin coat and disease risk, as well as the underlying mechanism.

zoology↗

The Crucial Role of CTCF in Mitotic Progression during Early Development of Sea Urchin.

CCCTC-binding factor (CTCF), an insulator protein with 11 zinc fingers, is enriched at the boundaries of topologically associated domains (TADs) in eukaryotic genomes. In this study, we isolated and analyzed the cDNAs encoding HpCTCF, the CTCF homolog in the sea urchin Hemicentrotus pulcherrimus, to investigate its expression patterns and functions during early development of sea urchin. HpCTCF contains nine zinc fingers corresponding to fingers 2-10 of the vertebrate CTCF. The expression pattern analysis revealed that HpCTCF mRNA was detected at all developmental stages and in the entire embryo. Upon expressing the HpCTCF-GFP fusion protein in early embryos, we observed its uniform distribution within interphase nuclei. However, during mitosis, it disappeared from the chromosomes and subsequently reassembled on the chromosome during telophase. Moreover, the morpholino-mediated knockdown of HpCTCF resulted in mitotic arrest during the morula-to-blastula stage. Most of the arrested chromosomes were not phospholylated at serine 10 of histone H3, indicating that mitosis was arrested at the telophase by HpCTCF depletion. Furthermore, impaired sister chromatid segregation was observed using time-lapse imaging of HpCTCF-knockdown embryos. Thus, HpCTCF is essential for mitotic progression during the early development of sea urchins, especially during the telophase-to-interphase transition. However, the normal development of pluteus larvae in CRISPR-mediated HpCTCF knockout embryos suggests that disruption of zygotic HpCTCF expression has little effect on embryonic and larval development.

developmental biology↗

Detailed profiling with MaChIAto reveals various genomic and epigenomic features affecting the efficacy of knock-out, short homology-based knock-in and Prime Editing

Highly efficient gene knock-out and knock-in have been achieved by harnessing CRISPR-Cas9 and its advanced technologies such as Prime Editor. In addition, various bioinformatics resources have become available to quantify and qualify the efficiency and accuracy of CRISPR edits, which significantly increased the user-friendliness of the general next-generation sequencing (NGS) analysis in the context of genome editing. However, there is no specialized and integrated software for investigating the preference in the genomic context involved in the efficiency and accuracy of genome editing using CRISPR-Cas9 and beyond. Here, we address this issue by establishing a novel analysis platform of NGS data for profiling the outcome of template-free knock- out and short homology-based editing, named MaChIAto (Microhomology- associated Chromosomal Integration/editing Analysis tools) (https://github.com/KazukiNakamae/MaChIAto). MaChIAto accommodates the classification and profiling of the NGS reads to uncover the tendency of the corresponding method of genome editing. In the profiling function, MaChIAto can summarize the mutation patterns along with the editing efficiency, and > 70 kinds of feature analysis, e.g., correlation analysis with thermodynamics and secondary structure parameters, are available. Additionally, the classifying function of MaChIAto is based on, but much stricter than, that of the existing tool, which is achieved by implementing a novel method of parameter adaptation utilizing Bayesian optimization. To demonstrate the functionality of MaChIAto, we analyzed the NGS data of knock- out, short homology-based knock-in, and Prime Editing. We confirmed that some features of (epi-)genomic context affected the efficiency and accuracy. These results show that MaChIAto is a helpful tool for understanding the best design for CRISPR edits. More importantly, it is the first tool for discovering features in the short homology-based knock-in outcomes. MaChIAto would help researchers profile editing data and generate prediction models for CRISPR edits, further contributing to revealing a "black box" process to produce a variety of CRISPR and Prime Editing outcomes.

bioinformatics↗

Double-layered two-directional somatopleural cell migration during chicken body wall development revealed with local fluorescent tissue labeling

The ventral body wall is derived from the somatic layer of the lateral plate mesoderm, somatopleure, and somite. The primary ventral body wall is formed as a result of the lateral growth of the somatopleure. The secondary body wall is generated through the migration of somitic cells into the somatopleure. While it is reported that the cervical somatopleural cells migrate caudally to the thoracic region during body wall development, the migration of the thoracic somatopleural cells has not been elucidated. To investigate the migration behavior of the somatopleural cells in the thorax during chicken ventral body wall development, we labeled the thoracic somatopleural cells of one somite wide by DiI labeling or gene transfection of enhanced green fluorescent protein and observed the three-dimensional distribution of the labeled cells with the tissue-clearing technique FRUIT. Our labeling experiments revealed the rostral migration of the somatopleural cells into a deep part of the thoracic body wall in embryonic day 6.5 chickens. For embryonic day 8.5 chickens, these deep migrating somatopleural cells were found around the sternal ribs. Thus, we identified the double-layered two-directional migrating pathways of the somatopleural cells: the rostral migration of the deep somatopleural cells and the lateral migration of the superficial somatopleural cells. Our findings imply that the rostral migration of deep somatopleural cells and the lateral migration of superficial ones might be associated with the developing sternal ribs and the innervation of the thoracic cutaneous nerves, respectively. Mini-abstractDouble-layered two-directional migrations of the somatopleural cells in the thoracic body wall during chicken development were revealed by one-somite-wide labeling of the somatopleure.

developmental biology↗

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↗

Insulator Activities of Nucleosome-Excluding DNA Sequences Without Bound Chromatin Looping Proteins

Chromosomes consist of various domains with different transcriptional activities separated by chromatin boundary sequences such as insulator sequences. Recent studies suggested that CTCF or other chromatin loop-forming protein binding sequences represented typical insulators. Alternatively, some long nucleosome-excluding DNA sequences were also reported to exhibit insulator activities in yeast and sea urchin chromosomes although specific binding of loop-forming proteins were not expected for them. However, the mechanism of the insulator activities of these sequences and the possibilities of similar insulators existing in other organisms remained unclear. In this study, we first constructed and performed simulations of a coarse-grained chromatin model containing nucleosome-rich and nucleosome-excluding DNA regions. We found that a long nucleosome-excluding region between two nucleosome-rich regions could markedly hinder the associations of two neighboring chromatin regions owing to the stronger long-term-averaged rigidity of the nucleosome-excluding region compared to that of nucleosome-rich regions. Subsequent analysis of the genome wide nucleosome positioning, protein binding, and DNA rigidity in human cells revealed that some nucleosome-excluding rigid DNA sequences without bound chromatin looping proteins could exhibit insulator activities, functioning as chromatin boundaries in various regions of human chromosomes.

genomics↗