Biology subjects

Matsui, Y.

Publications and source records attributed to Matsui, Y..

35 records · Page 2Linked to original sources

bioRxiv2023

Pgc-1α is an exercise-responsive regulator of myosteatosis in older individuals

Accumulated fat in skeletal muscle, common in sedentary older individuals, compromises skeletal muscle health and function. Mechanistic understanding of how physical activity levels dictate fat accumulation represents a critical step towards establishment of therapies that promote healthy aging. Using a network paradigm that characterized the transcriptomic response of aged muscle to exercise versus immobilization protocols, this study uncovered a novel molecular cascade that regulates the fate of fibro-adipogenic progenitors (FAPs), the cell population primarily responsible for the fat accumulation. Specifically, gene set enrichment analyses (GSEA) with network propagation revealed Pgc1 as a functional hub of a large gene regulatory network underlying the regulation of FAPs by physical activity. Integrated in silico and in situ approaches to induce Pgc-1 overexpression promoted mitochondrial fatty acid oxidation and inhibited FAPs adipogenesis. These findings suggest that Pgc1 is a master regulator by which physical activity regulates fat accumulation in aged skeletal muscle. GRAPHICAL ABSTRUCT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=173 SRC="FIGDIR/small/527478v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@5c4780org.highwire.dtl.DTLVardef@5a55ecorg.highwire.dtl.DTLVardef@bf1f16org.highwire.dtl.DTLVardef@192172e_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

bioRxiv2023

Network-based cytokine inference implicates Oncostatin M as a driver of knee osteoarthritis

Inflammatory cytokines released by the synovium after trauma disturb the gene regulatory network and have been implicated in the pathophysiology of osteoarthritis. A mechanistic understanding of how aging perturbs this process can help identify novel interventions. Here, we introduced network paradigms to simulate cytokine-mediated pathological communication between the synovium and cartilage. Cartilage-specific network analysis of injured young and aged murine knees revealed aberrant matrix remodeling as a transcriptomic response unique to aged knees displaying accelerated cartilage degradation. Next, network-based cytokine inference with pharmacological manipulation uncovered IL6 family member, Oncostatin M, as a driver for the aberrant matrix remodeling. By implementing a phenotypic drug discovery approach, we identified that the activation of Oncostatin M recapitulated "inflammation" phenotype of knee osteoarthritis and highlighted high-value targets for drug development and repurposing. These findings offer translational opportunities targeting the inflammation-driven osteoarthritis phenotype. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC="FIGDIR/small/525463v3_ufig1.gif" ALT="Figure 1"> View larger version (67K): org.highwire.dtl.DTLVardef@21b702org.highwire.dtl.DTLVardef@1761dd1org.highwire.dtl.DTLVardef@19f9fc2org.highwire.dtl.DTLVardef@b1a993_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

bioRxiv2022

Snip1-PRC2 governs the intrinsic apoptosis program in the developing brain

Brain development requires the intricate balance between division, death, and differentiation of neural progenitor cells (NPCs). Here, we report the discovery of Snip1 as a key regulator of these NPC phases. The conditional deletion of Snip1 in the mouse embryonic brain causes dysplasia with robust induction of caspase 9-dependent apoptosis. In NPCs, Snip1 suppresses the genetic programs of apoptosis and developmental signaling pathways and promotes the genetic programs of cell cycle, neurogenesis, and cortical development. Mechanistically, Snip1 binds to the Polycomb complex PRC2, co-occupies gene targets with PRC2, and regulates H3K27 marks. Deletion of PRC2 is sufficient to reduce apoptosis and brain dysplasia and partially restore genetic programs and tissue development in the Snip1-depleted brain. Our findings suggest that Snip1 exerts loci-dependent regulation of PRC2 and H3K27me3 to toggle between cell fates in the developing brain.

developmental biology↗

bioRxiv2022

Types of anomalies in two-dimensional video-based gait analysis in uncontrolled environments

Two-dimensional video-based pose estimation is a technique that can estimate human skeletal coordinates from video data alone. It is also being applied to gait analysis and, particularly, due to its simplicity of measurement, it has the potential to be applied to the gait analysis of large populations. In contrast, it is considered difficult to completely homogenize the environment and settings during the measurement of large populations. Therefore, it is necessary to appropriately deal with technical errors that are not related to the biological factors of interest. In this study, by analyzing a large cohort database, we have identified four major types of anomalies that occur during gait analysis using OpenPose in uncontrolled environments: anatomical, biomechanical, and physical anomalies and errors due to estimation. We have also developed a workflow for identifying and correcting those anomalies and confirmed that the workflow is reproducible through simulation experiments. Our results will help obtain a comprehensive understanding of the anomalies to be addressed in a pre-processing for 2D video-based gait analysis of large populations. Author summaryGait is one of the important biomarkers of health conditions. With developing mobile health technologies, it is becoming easier to measure our health. However, to realize preventive medicine, establishing evidence is a critical issue, and we need to collect data from a large population. Two-dimensional video-based pose estimation can be a solution for the gait analysis of such a population. However, the technical accuracy and limitations of this analysis have not yet been sufficiently discussed. In this study, by analyzing the largest database currently available, we systematically identified four types of technical anomalies that occur during gait measurement: anatomical, biomechanical, and physical anomalies and errors dues to estimation. We have also shown how to deal with these issues and made solutions available as software so that researchers can reproduce them. In the future, increasing number of studies will use 2D video-based pose estimation to research health-related gait among large populations. We believe that our work will provide a guideline for researchers and clinicians involved in these studies to discuss design and algorithms.

physiology↗

bioRxiv2021

SARS-CoV-2 spike protein induces abnormal inflammatory blood clots neutralized by fibrin immunotherapy

Blood clots are a central feature of coronavirus disease-2019 (COVID-19) and can culminate in pulmonary embolism, stroke, and sudden death. However, it is not known how abnormal blood clots form in COVID-19 or why they occur even in asymptomatic and convalescent patients. Here we report that the Spike protein from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) binds to the blood coagulation factor fibrinogen and induces structurally abnormal blood clots with heightened proinflammatory activity. SARS-CoV-2 Spike virions enhanced fibrin-mediated microglia activation and induced fibrinogen-dependent lung pathology. COVID-19 patients had fibrin autoantibodies that persisted long after acute infection. Monoclonal antibody 5B8, targeting the cryptic inflammatory fibrin epitope, inhibited thromboinflammation. Our results reveal a procoagulant role for the SARS-CoV-2 Spike and propose fibrin-targeting interventions as a treatment for thromboinflammation in COVID-19. One-Sentence SummarySARS-CoV-2 spike induces structurally abnormal blood clots and thromboinflammation neutralized by a fibrin-targeting antibody.

immunology↗

bioRxiv2021

Epi-mutations for spermatogenic defects by maternal exposure to Di (2-ethylhexyl) phthalate

Exposure to environmental factors during fetal development may lead to epigenomic modifications in fetal germ cells, altering gene expression and promoting diseases in successive generations. In mouse, maternal exposure to Di (2-ethylhexyl) phthalate (DEHP) is known to induce defects in spermatogenesis in successive generations, but the mechanism(s) of impaired spermatogenesis are unclear. Here, we showed that maternal DEHP exposure results in DNA hypermethylation of promoters of spermatogenesis-related genes in fetal testicular germ cells in F1 mice, and hypermethylation of Hist1h2ba, Sycp1 and Taf7l, which are crucial for spermatogenesis, persisted from fetal testicular cells to adult spermatogonia, resulting in the downregulation of expression of these genes. Forced methylation of these gene promoters silenced expression of these loci in a reporter assay. Expression and methylation of those genes tended to be downregulated and increased, respectively in F2 spermatogonia following maternal DEHP exposure. These results suggested that DEHP-induced hypermethylation of Hist1h2ba, Sycp1 and Taf7l in fetal germ cells results in downregulation of these genes in spermatogonia and subsequent defects in spermatogenesis, at least in the F1 generation.

developmental biology↗

bioRxiv2021

Meta-analysis and multi-omics to elucidate pathogenic mechanisms of age-related knee osteoarthritis

Increased mechanistic insight into the pathogenesis of knee osteoarthritis (KOA) is needed to develop efficacious disease-modifying treatments. Though age-related pathogenic mechanisms are most relevant to the great majority of KOA seen clinically, the bulk of our mechanistic understanding of KOA has been derived using surgically induced post-traumatic OA (PTOA) models. Here, we took an integrated approach of meta-analysis and multi-omics to elucidate pathogenic mechanisms of age-related KOA in murine model. Protein-level data together with transcriptomic profiling revealed inflammation, autophagy, and cellular senescence as primary hallmarks of age-related KOA. Importantly, the molecular profiles of aged cartilage were unique from those in PTOA, with only 1% overlap between the two. At the nexus of aging hallmarks, Advanced Glycation End-Product (AGE)/Receptor for AGE emerged as intrinsically linked to age-related KOA. This pathway was further validated by mass spectrometry. Collectively, these findings implicate dysregulation of AGE-RAGE signaling as a key driver of age-related KOA.

molecular biology↗

bioRxiv2020

RoDiCE: Robust differential protein co-expression analysis for cancer complexome

MotivationThe full spectrum of abnormalities in cancer-associated protein complexes remains largely unknown. Comparing the co-expression structure of each protein complex between tumor and healthy cells may provide insights regarding cancer-specific protein dysfunction. However, the technical limitations of mass spectrometry-based proteomics, including contamination with biological protein variants, causes noise that leads to non-negligible over- (or under-) estimating co-expression. ResultsWe propose a robust algorithm for identifying protein complex aberrations in cancer based on differential protein co-expression testing. Our method based on a copula is sufficient for improving identification accuracy with noisy data compared to conventional linear correlation-based approaches. As an application, we use large-scale proteomic data from renal cancer to show that important protein complexes, regulatory signaling pathways, and drug targets can be identified. The proposed approach surpasses traditional linear correlations to provide insights into higher order differential co-expression structures. Availability and Implementationhttps://github.com/ymatts/RoDiCE.

bioinformatics↗

bioRxiv2020

Single-cell dynamics of pannexin-1-facilitated programmed ATP loss during apoptosis

ATP is essential for all living cells. However, how dead cells lose ATP has not been well investigated. In this study, we developed new FRET biosensors for dual imaging of intracellular ATP level and caspase-3 activity in single apoptotic cultured human cells. We show that the cytosolic ATP level starts to decrease immediately after the activation of caspase-3, and this process is completed typically within 2 hours. The ATP decrease was facilitated by caspase-dependent cleavage of the plasma membrane channel pannexin-1, indicating that the intracellular decrease of the apoptotic cell is a "programmed" process. Apoptotic cells deficient of pannexin-1 sustained the ability to produce ATP through glycolysis and to consume ATP, and did not stop wasting glucose much longer period than normal apoptotic cells. Thus, the pannexin-1 plays a role in arresting the metabolic activity of dead apoptotic cells, most likely through facilitating the loss of intracellular ATP. (148 words)

cell biology↗

bioRxiv2019

Drosophila models of pathogenic copy-number variant genes show global and non-neuronal defects during development

While rare pathogenic copy-number variants (CNVs) are associated with both neuronal and non-neuronal phenotypes, functional studies evaluating these regions have focused on the molecular basis of neuronal defects. We report a systematic functional analysis of non-neuronal defects for homologs of 59 genes within ten pathogenic CNVs and 20 neurodevelopmental genes in Drosophila melanogaster. Using wing-specific knockdown of 136 RNA interference lines, we identified qualitative and quantitative phenotypes in 72/79 homologs, including 21 lines with severe wing defects and six lines with lethality. In fact, we found that 10/31 homologs of CNV genes also showed complete or partial lethality at larval or pupal stages with ubiquitous knockdown. Comparisons between eye and wing-specific knockdown of 37/45 homologs showed both neuronal and non-neuronal defects, but with no correlation in the severity of defects. We further observed disruptions in cell proliferation and apoptosis in larval wing discs for 23/27 homologs, and altered Wnt, Hedgehog and Notch signaling for 9/14 homologs, including AATF/Aatf, PPP4C/Pp4-19C, and KIF11/Klp61F. These findings were further supported by tissue-specific differences in expression patterns of human CNV genes, as well as connectivity of CNV genes to signaling pathway genes in brain, heart and kidney-specific networks. Our findings suggest that multiple genes within each CNV differentially affect both global and tissue-specific developmental processes within conserved pathways, and that their roles are not restricted to neuronal functions. AUTHOR SUMMARYRare copy-number variants (CNVs), or large deletions and duplications in the genome, are associated with both neuronal and non-neuronal clinical features. Previous functional studies for these disorders have primarily focused on understanding the cellular mechanisms for neurological and behavioral phenotypes. To understand how genes within these CNVs contribute to developmental defects in non-neuronal tissues, we assessed 79 homologs of CNV and known neurodevelopmental genes in Drosophila models. We found that most homologs showed developmental defects when knocked down in the adult fly wing, ranging from mild size changes to severe wrinkled wings or lethality. Although a majority of homologs tested showed defects when knocked down specifically in wings and eyes, we found no correlation in the severity of the observed defects in these two tissues. A subset of the homologs showed disruptions in cellular processes in the developing fly wing, including alterations in cell proliferation, apoptosis, and cellular signaling pathways. Furthermore, human CNV genes also showed differences in gene expression patterns and interactions with signaling pathway genes across multiple human tissues. Our findings suggest that genes within CNV disorders affect global developmental processes in both neuronal and non-neuronal tissues.

genomics↗

bioRxiv2019

Correlation between increased atrial expression of genes related to fatty acid metabolism and autophag y in patients with chronic atrial fibrillation

Atrial metabolic disturbance contributes to the onset and development of atrial fibrillation (AF). Autophagy plays a role in maintaining the cellular energy balance. We examined whether the altered atrial expression of genes related to fatty acid metabolism is linked to that related to autophagy in chronic AF. Right atrial tissue was obtained during heart surgery from 51 patients with sinus rhythm (SR, n=38) or chronic AF (n=13). Preoperative fasting serum free-fatty-acid levels were significantly higher in the AF patients. The atrial gene expression of fatty acid binding protein 3 (FABP3), which is involved in the cells fatty acid uptake and intracellular fatty acid transport, was significantly increased in AF patients compared to SR patients; in the SR patients it was positively correlated with the right atrial diameter and intra-atrial EMD, parameters of structural and electrical atrial remodeling that was evaluated by an echocardiography. In contrast, the two groups atrial contents of diacylglycerol (DAG), a toxic fatty acid metabolite, were comparable. Importantly, the atrial gene expression of microtubule-associated protein light chain 3 (LC3) was significantly increased in the AF patients, and autophagy-related genes including LC3 were positively correlated with the atrial expression of FABP3. In conclusion, in chronic AF patients, the atrial expression of FABP3 was upregulated in association with autophagy-related genes without altered atrial DAG content. Our findings may support the hypothesis that dysregulated cardiac fatty acid metabolism contributes to the progression of AF and induction of autophagy has a cardioprotective effect against cardiac lipotoxicity in chronic AF.

molecular biology↗

bioRxiv2019

Microbial community and geochemical analyses of trans-trench sediments for understanding the roles of hadal environments

Hadal trench bottom (>6,000 m below sea level) sediments harbor higher microbial cell abundance compared to adjacent abyssal plain sediments. This is supported by the accumulation of sedimentary organic matter (OM), facilitated by trench topography. However, the distribution of benthic microbes in different trench systems has not been explored yet. Here, we carried out small subunit ribosomal RNA gene tag sequencing for 92 sediment subsamples of seven abyssal and seven hadal sediment cores collected from three trench regions in the northwest Pacific Ocean: the Japan, Izu-Ogasawara, and Mariana Trenches. Tag-sequencing analyses showed specific distribution patterns of several phyla associated with oxygen and nitrate. The community structure was distinct between abyssal and hadal sediments, following geographic locations and factors represented by sediment depth. Co-occurrence network revealed six potential prokaryotic consortiums that covaried across regions. Our results further support that the endogenous OM cycle is driven by hadal currents and/or rapid burial shapes microbial community structures at trench bottom sites, in addition to vertical deposition from the surface ocean. Our trans-trench analysis highlights intra- and inter-trench distributions of microbial assemblages and geochemistry in surface seafloor sediments, providing novel insights into ultra-deep-sea microbial ecology, one of the last frontiers on our planet.

microbiology↗

bioRxiv2019

Isolation of an archaeon at the prokaryote-eukaryote interface

The origin of eukaryotes remains enigmatic. Current data suggests that eukaryotes may have risen from an archaeal lineage known as \"Asgard archaea\". Despite the eukaryote-like genomic features found in these archaea, the evolutionary transition from archaea to eukaryotes remains unclear due to the lack of cultured representatives and corresponding physiological insight. Here we report the decade-long isolation of a Lokiarchaeota-related Asgard archaeon from deep marine sediment. The archaeon, \"Candidatus Prometheoarchaeum syntrophicum strain MK-D1\", is an anaerobic, extremely slow-growing, small cocci ([~]550 nm), that degrades amino acids through syntrophy. Although eukaryote-like intracellular complexities have been proposed for Asgard archaea, the isolate has no visible organella-like structure. Ca. P. syntrophicum instead displays morphological complexity - unique long, and often, branching protrusions. Based on cultivation and genomics, we propose an \"Entangle-Engulf-Enslave (E3) model\" for eukaryogenesis through archaea-alphaproteobacteria symbiosis mediated by the physical complexities and metabolic dependency of the hosting archaeon.

microbiology↗

bioRxiv2019

Paternal age affects offspring's behavior possibly via an epigenetic mechanism recruiting a transcriptional repressor REST

Advanced paternal age has deleterious effects on mental health of next generation. Using a mouse model, we have confirmed that offspring derived from aged fathers showed impairments in behavior and abnormalities in the brain structure and activity. Comprehensive target DNA methylome analyses revealed in aged sperm more hypo-methylated genomic regions, in which REST/NRSF binding motif was enriched. Gene set enrichment analyses also identified enrichment of "REST/NRSF target genes", in addition to "Late-fetal genes" and autism spectrum disorder-related "SFARI genes", in up-regulated genes of developing brains from aged father. Indeed, gene sets near hypo-methylated genomic regions with REST/NRSF binding motif were also enriched in up-regulated genes of developing brains. Taken altogether, DNA hypo-methylation due to paternal aging in sperm will induce leaky expression of REST/NRSF target genes in the developing brain, thereby causing neuronal abnormalities and subsequent behavioral alteration in offspring.

neuroscience↗

bioRxiv2018

GIMLET: Identifying Biological Modulators in Context-Specific Gene Regulation Using Local Energy Statistics

The regulation of transcription factor activity dynamically changes across cellular conditions and disease subtypes. The identification of biological modulators contributing to context-specific gene regulation is one of the challenging tasks in systems biology, which is necessary to understand and control cellular responses across different genetic backgrounds and environmental conditions. Previous approaches for identifying biological modulators from gene expression data were restricted to the capturing of a particular type of a three-way dependency among a regulator, its target gene, and a modulator; these methods cannot describe the complex regulation structure, such as when multiple regulators, their target genes, and modulators are functionally related. Here, we propose a statistical method for identifying biological modulators by capturing multivariate local dependencies, based on energy statistics, which is a class of statistics based on distances. Subsequently, our method assigns a measure of statistical significance to each candidate modulator through a permutation test. We compared our approach with that of a leading competitor for identifying modulators, and illustrated its performance through both simulations and real data analysis. Our method, entitled genome-wide identification of modulators using local energy statistical test (GIMLET), is implemented with R ([≥] 3.2.2) and is available from github (https://github.com/tshimam/GIMLET).

bioinformatics↗

bioRxiv2018

A Network of Networks Approach for Modeling Interconnected Brain Tissue-Specific Networks

MotivationRecent sequence-based analyses have identified a lot of gene variants that may contribute to neurogenetic disorders such as autism spectrum disorder and schizophrenia. Several state-of-the-art network-based analyses have been proposed for mechanical understanding of genetic variants in neurogenetic disorders. However, these methods were mainly designed for modeling and analyzing single networks that do not interact with or depend on other networks, and thus cannot capture the properties between interdependent systems in brain-specific tissues, circuits, and regions which are connected each other and affect behavior and cognitive processes.\n\nResultsWe introduce a novel and efficient framework, called a \"Network of Networks\" (NoN) approach, to infer the interconnectivity structure between multiple networks where the response and the predictor variables are topological information matrices of given networks. We also propose Graph-Oriented SParsE Learning (GOSPEL), a new sparse structural learning algorithm for network graph data to identify a subset of the topological information matrices of the predictors related to the response. We demonstrate on simulated data that GOSPEL outperforms existing kernel-based algorithms in terms of F-measure. On real data from human brain region-specific functional networks associated with the autism risk genes, we show that the NoN model provides insights on the autism-associated interconnectivity structure between functional interaction networks and a comprehensive understanding of the genetic basis of autism across diverse regions of the brain.\n\nAvailabilityOur software is available from https://github.com/infinite-point/GOSPEL.\n\nContactkawakubo@med.nagoya-u.ac.jp, shimamura@med.nagoya-u.ac.jp\n\nSupplementary informationSupplementary data are available at Bioinformatics online.

systems biology↗

bioRxiv2017

Tumor subclonal progression model for cancer hallmark acquisition

Recent advances in the methods for reconstruction of cancer evolutionary trajectories opened up the prospects of deciphering the subclonal populations and their evolutionary architectures within cancer ecosystems. An important challenge of the cancer evolution studies is how to connect genetic aberrations in subclones to a clinically interpretable and actionable target in the subclones for individual patients. In this study, our aim is to develop a novel method for constructing a model of tumor subclonal progression in terms of cancer hallmark acquisition using multiregional sequencing data. We prepare a subclonal evolutionary tree inferred from variant allele frequencies and estimate pathway alteration probabilities from large-scale cohort genomic data. We then construct an evolutionary tree of pathway alterations that takes into account selectivity of pathway alterations via selectivity score. We show the effectiveness of our method on a dataset of clear cell renal cell carcinomas.

bioinformatics↗