Biology subjects

Noguchi, M.

Publications and source records attributed to Noguchi, M..

14 recordsLinked to original sources

bioRxiv2026

HNRNPC-mediated RNA processing promotes VHL-associated excessive vasculogenesis in von Hippel-Lindau syndrome revealed from patient-derived blood vessel models

Von Hippel-Lindau Syndrome (VHLS) is an inherited disorder characterized by excessive vascularization, which contributes to the development of hemangioblastomas and benign or malignant tumors, as well as renal cell carcinoma (RCC) and cysts in multiple organs. VHLS is caused by mutations in VHL tumor suppressor gene, which encodes a component of an E3 ubiquitin ligase complex. Although therapeutic agents targeting hypoxia-inducible factor 2 alpha (HIF2A), which is stabilized by VHL loss and promotes tumor angiogenesis, have been approved for clinical use, their therapeutic response remains limited in RCC patients associated with VHLS. Therefore, there is an unmet need for the development of alternative therapeutic approaches independent of HIF2A. Here, we establish a human iPSCs-based model of VHLS-associated excessive vasculogenesis using induced pluripotent stem cells (iPSCs) derived from VHLS patients and VHL-edited isogenic iPSC lines. Vascular cells (VCs) differentiated from these VHLS-specific iPSCs exhibited excessive blood vessel formation compared to healthy donor-derived VCs, leading to vascular lesion formation characterized by abundant blood vessels and abnormal cellular growth in vivo. Mechanistically, RNA-binding proteins (RBPs) were preferentially stabilized in the patient-VCs. Among these RBPs, the stabilization of heterogeneous nuclear ribonucleoprotein C1/C2 (HNRNPC), which is a substrate for pVHL-mediated protein degradation independent of HIF2A expression, was critical for the dysregulated vascularization caused by VHL inactivation in this model. These findings provide an iPSCs-derived vascular platform to elucidate VHLS mechanisms and identify HNRNPC as a potential therapeutic target for VHL-driven vascular lesion formations through an HIF2A-independent mechanism.

cell biology↗

bioRxiv2026

Global distributions and plant associations of the ecologically diverse ascomycete order Helotiales

Background Fungi in plant root systems are key to understanding the dynamics and functioning of terrestrial ecosystems. Whereas our knowledge of below-ground plant-fungus symbioses has derived mainly from studies of mycorrhizal and pathogenic fungi, recent studies have uncovered an unexpected diversity of ecological niches occupied by root-associated fungi. The fungal order Helotiales is conspicuous in this respect because this predominantly root-associated taxon encompasses a broad ecological spectrum, ranging from saprotrophic and pathogenic fungi to endophytic and mycorrhizal fungi with plant growth-promoting functions. In this study, we integrated a worldwide dataset of 1,996 Helotiales Species Hypotheses (i.e., species-level taxa tentatively defined based on DNA sequences) detected in roots of 362 plant genera representing 117 families and 47 orders, and systematically quantified the specificity of Helotiales-plant associations. Results The analysis of 37,688 unique occurrence records of Helotiales fungi across 1,940 global sampling locations revealed highly structured associations between Helotiales genera and plant lineages, exemplified by the strong specificity of Hyaloscypha, Oidiodendron, and Phialocephala for Pinales and that of Glutinomyces for Fagales, even after statistically controlling background biogeographic patterns. At the Species-Hypothesis-level analysis, major clades within the Helotiales phylogeny consistently exhibited high specificity for Pinaceae, whereas highly specific associations with other ectomycorrhizal, arbuscular mycorrhizal, and nonmycorrhizal plants were restricted to small terminal clades of the fungal phylogeny. Conclusions The integration of ecological specificity and phylogenetic analyses suggests the possibility that Helotiales fungi established close associations with Pinaceae early in their evolutionary history and subsequently underwent host shifts to diverse angiosperm lineages. Given the emerging evidence that Helotiales fungi play pivotal ecological and physiological roles in plant root systems, these statistical insights into Helotiales-plant associations provide a fundamental basis for understanding the evolutionary history and functioning of terrestrial ecosystems.

microbiology↗

bioRxiv2026

Environmental filtering and host identity collectively shape root-associated microbiomes of Ericaceae and ectomycorrhizal plants in fumarole fields

Background Symbiosis with microbes is a key strategy that has enabled plants to colonize extreme environments. Since the benefits conferred by root-associated microbes depend on both environmental conditions and host-microbe combinations, plant adaptation to harsh environments is closely linked to the assembly of root microbial communities. Understanding how environmental and host filtering jointly shape these communities is therefore fundamental to elucidating the mechanisms underlying plant adaptation to extreme environments. Results In this study, we investigated the differentiation of root-associated prokaryotic and fungal communities and individual operational taxonomic units (OTUs) across two contrasting habitats surrounding fumaroles, solfatara-field and forest-edge habitats, and six dominant Ericaceae and ectomycorrhizal plant taxa. Prokaryotic and fungal OTUs rarely exhibited strong preferences for both habitat and host identity. Instead, many of prokaryotic and fungal OTUs specialized to one of these niches, collectively generating root microbial communities differentiated by both factors. Nonetheless, striking specializations in habitat and host niches were observed in the fungal family Hyaloscyphaceae (Helotiales). To gain insight into the evolutionary basis of microbial specialization, we examined phylogenetic signals in preference phenotypes. The resulting weak phylogenetic signals in these preference phenotypes further suggest that this fungal clade has undergone substantial ecological divergence. Conclusion Overall, our findings indicate that root-associated microbial communities in extreme environments are assembled through the accumulation of microbial taxa specialized to either habitat or host, and that strong ecological specialization in fungi can arise with little phylogenetic constraint.

microbiology↗

bioRxiv2025

Ataxia-Telangiectasia Mutated Inhibition Enhances Adeno-Associated Virus-Mediated Knock-in Efficiency in Pig Zygotes

A persistent global shortage of transplantable organs has renewed interest in pigs as donors for xenotransplantation and hosts for interspecies organogenesis considering their physiology closely resembles that of humans. Such applications require pigs harboring genetic modifications, including knockouts, human transgenes, and conditional alleles. Although such complex allele combinations can be assembled by sequential editing of fetal fibroblasts, followed by somatic cell nuclear transfer (SCNT), SCNT is often associated with developmental abnormalities. Direct genome editing of pig zygotes offers an alternative route; however, achieving long-fragment knock-in, particularly at multiple loci, remains challenging. Here, adeno-associated virus (AAV) donor vectors for long-fragment knock-in in pig zygotes were evaluated, and tested whether transient inhibition of ataxia-telangiectasia mutated (ATM), which becomes overactivated during AAV transduction, could enhance knock-in efficiency. AAV6 donors supported efficient ACTB-mEGFP knock-in (33%), whereas short-term treatment with the ATM inhibitor AZ32 increased the efficiency to 66%. In addition, AZ32 enhanced simultaneous double knock-in at ACTB and UBB, generating a higher proportion of double-positive blastocysts (52% vs. 19% in controls), without affecting blastocyst formation rates or total cell numbers. Embryo transfer yielded ACTB-mEGFP and UBB-mScarlet-I3 double knock-in fetuses (33%), including an F0 fetus composed almost entirely of double knock-in cells. These results demonstrate that combining AAV donors with transient ATM inhibition is an efficient strategy for long-fragment knock-in at multiple loci in pigs.

bioengineering↗

bioRxiv2024

Mycorrhizal and endophytic fungi structure contrasting but interdependent assembly processes in forest below-ground symbiosis

Interactions between plants and diverse root-associated fungi are essential drivers of forest ecosystem dynamics. The nature of the symbiosis in root systems is potentially dependent on multiple ecological factors/processes such as host/symbiont specificity, background soil microbiome structure, inter-root sharing/dispersal of symbionts, and fungus-fungus interactions within fine roots. Nonetheless, it has remained a major challenge to reveal the mechanisms by which those multiple factors/processes determine the assembly of mycorrhizal and endophytic fungal communities. Based on a framework of joint species distribution modeling, we here examined how root-associated fungal community structure was collectively formed through filtering by host plants, associations with background soil fungi, spatial autocorrelation, and symbiont-symbiont interactions. In our analysis targeting 1,615 root-tip samples collected in a cool-temperate forest dominated by ectomycorrhizal plants, statistical models including all the four ecological factors/processes best explained the fine-scale community structure of root-associated fungi. Meanwhile, among partial models including subsets of those ecological factors/processes, those including background soil microbiome structure and within-root fungus-fungus interactions showed the highest performance. When fine-root distributions of respective fugal species/taxa were examined, ectomycorrhizal fungi tended to show stronger associations with background soil community structure and stronger spatially-autocorrelated patterns than other fungal guilds. In contrast, the distributions of root-endophytic fungi were inferred to depend greatly on fungus-fungus interactions. A network statistical analysis further suggested that some endophytic fungi, such as those belonging to the ascomycete genera Phialocephala and Leptodontidium, were involved in webs of positive and negative interactions with other root-associated fungi. These results suggest that basic assembly rules can differ between mycorrhizal and endophytic fungi, both of which are major components of forest ecosystems. Consequently, knowledge of how multiple ecological factors/processes differentially drive the assembly of multiple fungal functional guilds is indispensable for comprehensively understanding the mechanisms by which terrestrial ecosystem dynamics are organized by plant-fungal symbiosis.

ecology↗

bioRxiv2023

Complete suspension culture of human induced pluripotent stem cells supplemented with suppressors of spontaneous differentiation

Human induced pluripotent stem cells (hiPSCs) are promising resources for producing various types of tissues in regenerative medicine; however, the improvement in a scalable culture system that can precisely control the cellular status of hiPSCs is needed. Utilizing suspension culture without microcarriers or special materials allows for massive production, automation, cost-effectiveness, and safety assurance in industrialized regenerative medicine. Here, we found that hiPSCs cultured in suspension conditions with continuous agitation without any microcarriers or extracellular matrix components were more prone to spontaneous differentiation than those cultured in conventional adherent conditions. Adding PKC{beta} and Wnt signaling pathway inhibitors in the suspension conditions suppressed the spontaneous differentiation of hiPSCs into ectoderm and mesendoderm, respectively. In these conditions, we successfully completed the culture processes of hiPSCs including the generation of hiPSCs from peripheral blood mononuclear cells with the expansion of bulk population and single-cell sorted clones, long-term culture with robust self-renewal characteristics, single-cell cloning, direct cryopreservation from suspension culture and their successful recovery, and efficient mass production of a clinical-grade hiPSC line. Our results demonstrate that precise control of the cellular status in suspension culture conditions paves the way for their stable and automated clinical application.

bioengineering↗

bioRxiv2023

Exploring the genetic diversity of the Japanese Population: Insights from a Large-Scale Whole Genome Sequencing Analysis

The Japanese archipelago is a terminal location for human migration, and the contemporary Japanese people represent a unique population whose genomic diversity has been shaped by multiple migrations from Eurasia. Through high-coverage whole-genome sequencing (WGS) analysis of 9,850 samples from the National Center Biobank Network, we analyzed the genomic characteristics that define the genetic makeup of the modern Japanese population from a population genetics perspective. The dataset comprised populations from the Ryukyu Islands and other parts of the Japanese archipelago (Hondo). Low frequency detrimental or pathogenic variants were found in these populations. The Hondo population underwent two episodes of population decline during the Jomon period, corresponding to the Late Neolithic, and the Edo period, corresponding to the Early Modern era, while the Ryukyu population experienced a population decline during the shell midden period of the Late Neolithic in this region. Genes related to alcohol and lipid metabolism were affected by positive natural selection. Two genes related to alcohol metabolism were found to be 12,500 years out of phase with the time when they began to be affected by positive natural selection; this finding indicates that the genomic diversity of Japanese people has been shaped by events closely related to agriculture and food production. Author summaryThe human population in the Japanese archipelago exhibits significant genetic diversity, with the Ryukyu Islands and other parts of the archipelago (Hondo) having undergone distinct evolutionary paths that have contributed to the genetic divergence of the populations in each region. In this study, whole genome sequencing of healthy individuals from national research hospital biobanks was utilized to investigate the genetic diversity of the Japanese population. Haplotypes were inferred from the genomic data, and a thorough population genetic analysis was conducted. The results indicated not only genetic differentiation between Hondo and the Ryukyu Islands, but also marked differences in past population size. In addition, gene genealogies were inferred from the haplotypes, and the patterns were scrutinized for evidence of natural selection. This analysis revealed unique traces of natural selection in East Asian populations, many of which were believed to be linked to dietary changes brought about by agriculture and food production.

genomics↗

bioRxiv2023

Defining T cell receptor repertoires using nanovial-based affinity and functional screening

The ability to selectively bind to antigenic peptides and secrete cytokines can define populations of cells with therapeutic potential in emerging T cell receptor (TCR) immunotherapies. We leverage cavity-containing hydrogel microparticles, called nanovials, each coated with millions of peptide-major histocompatibility complex (pMHC) monomers to isolate antigen-reactive T cells. T cells are captured and activated by pMHCs and secrete cytokines on nanovials, allowing sorting based on both affinity and function. The TCRs of sorted cells on nanovials are sequenced, recovering paired {beta}-chains using microfluidic emulsion-based single-cell sequencing. By labeling nanovials having different pMHCs with unique oligonucleotide-barcodes we could link TCR sequence to targets with 100% accuracy. We identified with high specificity an expanded repertoire of functional TCRs targeting viral antigens compared to standard techniques. One-sentence SummaryAffinity and secretion-based screening of antigen-specific T cells using nanovials defines a functional TCR repertoire

bioengineering↗

bioRxiv2022

AUTS2 gene dosage affects synaptic AMPA receptors via a local dendritic spine AUTS2-TTC3-AKT-mTORC1 signaling dysfunction

The Human 1.2-Mb AUTS2 locus on chromosome 7q11.22 encodes a 1259-aa full-length protein, and a 711-aa C-terminal isoform. Functions of these AUTS2 proteins are only partly known. The major traits found in patients displaying AUTS2 locus mutations are Intellectual Disabilities, microcephaly attention deficit hyperactivity disorder (ADHD) (54%), and autistic traits. Furthermore, AUTS2 common variants were recently found associated to alcohol consumption and dyslexia using GWAS approaches. Auts2 localizes mainly in cell nuclei. We evidenced by super-resolution that Auts2 is present in dendritic spines. Auts2 interacts with Ttc3, the Akt2 E3 ligase, and negatively regulates Akt2 ubiquitination. Auts2 haploinsufficiency affects Akt/mTorc1 pathway with a decrease in AMPA and NMDA receptor subunits and in synaptic currents. Akt2 injection in postsynaptic neurons is sufficient to reverse changes in synaptic currents generated by Auts2 haploinsufficiency. Using chromosome engineering based on targeted meiotic recombination, we generated two mouse models with Auts2 locus deletion and duplication. Deleted Auts2 locus mice display stereotypies (rearing), perseveration and abnormal recognition memory. Duplicated Auts2 locus mice display similar perseveration and abnormal recognition memory but also a decrease in cued and contextual fear memory. Gene dosage induce changes in brain sub-region neuronal networks. In the thalamo-lateral amygdala pathway linked to cued fear memory, we found synaptic impairments linked to AMPA receptors, with a specific decrease in pAKT/total AKT ratio in duplicated Auts2 mice. Altogether, our study thereby provides a novel mechanistic and potentially therapeutic understanding of synaptic AKT/mTORC1 deregulated signaling and its related behavioral and cognitive phenotypes.

neuroscience↗

bioRxiv2022

Mobile elements in human population-specific genome and phenotype divergence

Mobile genetic elements (MEs) are heritable mutagens that contribute to divergence between lineages by recursively generating structural variants. ME variants (MEVs) are difficult to genotype, obscuring their impact on recent genome and trait diversification. We developed a tool that uses short-read sequence data to accurately genotype MEVs, enabling us to study them using statistical genetics methods in global human genomes. We observe population-specific differences in the distribution of Alu insertions that distinguish Japanese from other populations. We integrated MEVs with epigenomic and expression quantitative trait loci (eQTL) maps to determine how they impact traits. This reveals coherent patterns by which specific MEs regulate tissue-specific gene expression, including creating or attenuating enhancers and recruiting post-transcriptional regulators. We pinpoint MEVs as genetic causes of disease risk, including a LINE-1 insertion linked to keloid and other diseases of fibroblast inflammation, by introducing MEVs into the genome-wide association study (GWAS) framework. In addition to nominating previously-hidden MEVs as causes of human diseases, this work highlights MEs as accelerators of human population divergence and begins to decipher the semantics of MEs.

genetics↗

bioRxiv2021

Skeletal muscle releases extracellular vesicles with distinct protein and miRNA signatures that accumulate and function within the muscle microenvironment

Extracellular vesicles (EVs) contain various regulatory molecules and mediate intercellular communications. Although EVs are secreted from various cell types, including skeletal muscle cells, and present in the blood, their identity is poorly characterized in vivo, limiting the identification of their origin in the blood. Since the skeletal muscle is the largest organ in the body, it could substantially contribute to circulating EVs as their source. However, due to the lack of defined markers that distinguish SkM-EVs from others, whether the skeletal muscle releases EVs in vivo and how much the skeletal muscle-derived EVs (SkM-EVs) account for plasma EVs remain poorly understood. In this work, we perform quantitative proteomic analyses on EVs released from C2C12 cells and human iPS cell-derived myocytes and identify potential marker proteins that mark SkM-EVs. These markers we identified apply to in vivo tracking of SkM-EVs. The results show that skeletal muscle makes only a subtle contribution to plasma EVs as their source in both control and exercise conditions in mice. On the other hand, we demonstrate that SkM-EVs are concentrated in the skeletal muscle interstitium. Furthermore, we show that interstitium EVs are highly enriched with the muscle-specific miRNAs and repress the expression of the paired box transcription factor Pax7, a master regulator for myogenesis. Taken together, our findings reveal that the skeletal muscle releases exosome-like small EVs with distinct protein and miRNA profiles in vivo and that SkM-EVs mainly play a role within the muscle microenvironment where they accumulate.

physiology↗

bioRxiv2021

Retinoids rescue ceruloplasmin secretion and alleviate oxidative stress in Wilson's disease-specific hepatocytes

Wilsons disease (WD) is a copper metabolic disorder, which is caused by defective ATP7B function. Here, we have generated induced pluripotent stem cells (iPSCs) from WD patients carrying compound heterozygous mutations on ATP7B. ATP7B loss- and gain-of-functions were further manifested with ATP7B-deficient iPSCs and heterozygously-corrected R778L WD patient-derived iPSCs using CRISPR-Cas9-based gene editing. Transcriptome analysis identified abnormalities of retinoid signaling pathway and lipid metabolism in WD-specific hepatocytes. Although the expression level of ATP7B protein was variable among WD-specific hepatocytes, the expression and secretion of ceruloplasmin (Cp), which is a downstream copper carrier in plasma, were consistently decreased. Cp secretion-based drug screening identified all-trans retinoic acid (ATRA) as promising candidates for rescuing Cp secretion. ATRA also alleviated reactive oxygen species (ROS) production induced by lipid accumulation in WD-specific hepatocytes. Our patient-derived iPSC-based hepatic models provide potential therapeutics for liver steatosis in WD and other fatty liver diseases.

cell biology↗

bioRxiv2021

Aboveground biomass increments over 26 years (1993-2019) in an old-growth cool-temperate forest in northern Japan

Assessing long-term changes in biomass of old-growth forests is critical in evaluating forest ecosystem functions under a changing climate. Long-term biomass changes are the result of accumulated short-term changes, which can be affected by endogenous processes such as gap filling in small-scale canopy openings. Here, we used 26 years (1993-2019) of repeated tree census data in an old-growth, cool-temperate, deciduous mixed forest that contains three topographic units (riparian, denuded slope, and terrace) in northern Japan to document decadal changes in aboveground biomass (AGB) and their processes in relation to endogenous processes and climatic factors. AGB increased steadily over the 26 years in all topographic units, but different tree species contributed to the increase among the topographic units. AGB gain within each topographic unit exceeded AGB loss via tree mortality in most of the measurement periods despite substantial temporal variation in AGB loss. At the local scale, variations in AGB gain were partially explained by compensating growth of trees around canopy gaps. Climate affected the local-scale AGB gain: the gain was larger in the measurement periods with higher mean temperature during the current summer but smaller in those with higher mean temperature during the previous autumn, synchronously in all topographic units. The decadal climate trends of warming are likely to have contributed to the steady increase in AGB in this old-growth forest.

ecology↗

bioRxiv2019

Toxicokinetics of citreoviridin in vivo and in vitro.

Citreoviridin (CIT) produced by Penicillium citreonigrum as a secondary metabolite is a yellow rice toxin that has been reported to be related to acute cardiac beriberi; however, its toxicokinetics remain unclear. The present study elucidated the toxicokinetics through swine in vivo experiments and predicted the human toxicokinetics by a comparison with findings from in vitro experiments. Swine in vivo experiments revealed that CIT had a high bioavailability of more than 90%. In addition, it showed a large volume of distribution (1.005 {+/-} 0.195 L/kg) and long elimination half-life (17.7 {+/-} 3.3 h) in intravenous. These results suggested the possibility of a slow metabolism of CIT. An intestinal permeability study using the human cell line Caco-2 showed that CIT had a high permeability coefficient, suggesting it would be easily absorbed in human intestine, similar to its absorption in swine. The metabolite profiles were investigated by incubating CIT with S9 obtained from swine and humans. Hydroxylation, methylation, desaturation and dihydroxylation derivatives were detected as the predominant metabolites, and CIT glucuronide was produced slowly compared with above metabolites. A comparison of the peak area ratios obtained using quadrupole time-of-flight mass spectrometer showed that the rates of all of the main metabolites except for glucuronide produced using human S9 were three-fold higher than those obtained using swine S9. Furthermore, the elimination of CIT using human S9 was more rapid than when using swine S9, indicating that CIT would be metabolized faster in humans than in swine. These in vivo results suggested that CIT is easily absorbed in swine and persists in the body for a long duration. Furthermore, the CIT metabolism appeared to be faster in human liver than in swine liver in vitro, although the bioavailability of CIT was predicted to be similarly high in humans as in swine.

pharmacology and toxicology↗