Biology subjects

Fujita, A.

Publications and source records attributed to Fujita, A..

10 recordsLinked to original sources

bioRxiv2026

Modulation of human dorsal root ganglion neuron excitability by Nav1.7 inhibition

Nav1.7 voltage-gated sodium channels are strongly expressed in human primary pain-sensing neurons (nociceptors) and selective Nav1.7 inhibitors have been developed as possible therapeutic agents for treating pain, so far with disappointing clinical results. In contrast, a selective Nav1.8 channel inhibitor (suzetrigine) has had successful clinical trials. Because nociceptors express both Nav1.7 and Nav1.8 channels, it is of interest to compare effects of Nav1.7 and Nav1.8 inhibitors on the excitability of human nociceptors. To compare with previous results with suzetrigine, we characterized the effects of a selective Nav.7 inhibitor, AM-2099, on action potential generation and repetitive firing of dissociated human dorsal root ganglion neurons, studied at 37{degrees}C. Inhibition of Nav1.7 channels by 600 nM AM-2099 generally produced a substantial depolarizing shift of action potential threshold, an increase in rheobase, a decrease in action potential upstroke velocity, decrease in action potential peak, and prolongation of refractory period. Compared to inhibition of Nav1.8 channels, inhibition of Nav1.7 channels had larger effects on threshold and maximal upstroke velocity, while action potential peak was reduced similarly by both. Nav1.8 inhibition produced much more dramatic reduction of repetitive firing than Nav1.7 inhibition. The results show that although the excitability of human DRG neurons is affected by inhibition of Nav1.7 channels, most notably by an increase in threshold and increase in refractory period, repetitive firing of the neurons in response to strong stimuli is little affected.

neuroscience↗

bioRxiv2025

Genome editing of the flavanone 3-hydroxylase gene produces a green Perilla line with elevated luteolin accumulation

Perilla frutescens var. crispa is widely cultivated in East Asia and produces a diverse range of secondary metabolites with nutritional and medicinal value. Based on anthocyanin content, perilla is classified into red and green chemotypes. The anthocyanin biosynthetic pathway is highly conserved among plants, and the flavanone 3-hydroxylase gene (F3H) in red perilla is considered essential for this pathway. Here, we used CRISPR-Cas9 genome editing to generate novel Perilla lines with altered metabolite profiles. In four edited T plants, multiple biallelic indels, including a -3 bp in-frame deletion, were introduced at the target site. In the T generation, these mutations and the transgene segregated in a Mendelian manner, resulting in recovery of null-segregant plants. Metabolite analysis revealed strong suppression of anthocyanin biosynthesis and a significant increase in luteolin accumulation in edited lines compared with the wild type. Transcriptome analysis further confirmed the loss of F3H function, demonstrating a metabolic shift of the flavonoid pathway toward luteolin production. This study provides the first functional validation of F3H in perilla and highlights its potential application in breeding cultivars with controlled bioactive compound contents. Our findings also demonstrate practical strategies for implementing genome editing in non-model crops and developing high-value functional cultivars. Practitioner PointsO_LIEditing a single flavonoid biosynthetic gene (F3H) effectively alters pigment composition in perilla leaves. C_LIO_LIIncreased accumulation of luteolin-related compounds suggests potential for enhancing functional metabolites without complex pathway engineering. C_LIO_LIGenome editing offers a feasible tool for perilla improvement in breeding and functional food development. C_LI

plant biology↗

bioRxiv2025

Enabling wider access to human molecular neuroscience research in pain: A simple preservation method for human dorsal root ganglion neurons in Hibernate A media

The use of human dorsal root ganglion (DRG) from organ donors opens the door for research into the molecular biology and physiology of human nociceptors; however, there are barriers to working with this tissue including logistical difficulties and limited access. We present an approach using Hibernate media to temporarily store either whole DRGs or dissociated DRG neurons prior to culturing and functional testing. Dissociation of DRGs following temporary storage (4-16hrs) in Hibernate media resulted in similar neuronal and immune cell yield as acutely dissociated DRGs. Neurons derived from DRGs stored in Hibernate media prior to dissociation exhibited similar electrophysiological properties and capsaicin responses as acutely dissociated DRG neurons. Similarly, neurons from acutely dissociated DRGs stored in Hibernate media (>24hrs) and shipped to geographically distant laboratories produced neuronal cultures displaying comparable electrophysiological properties as acutely cultured neurons. This approach overcomes insurmountable logistical burdens and increases access to freshly recovered human DRGs.

neuroscience↗

bioRxiv2024

Transient residence of the repulsive client Shutdown in Yb bodies plays a critical role in Piwi-piRISC biogenesis and maintaining fertility

Nonmembranous organelles, such as Yb bodies in Drosophila ovarian somatic cells, form through liquid-liquid phase separation of scaffold proteins. Client proteins transiently accumulate in these organelles by binding to scaffolds. However, the regulation of this process is not well understood. Here, we investigate Shutdown, a client protein in Yb bodies, the site of Piwi-piRISC precursor (pre-Piwi-piRISC) formation. We found that Shutdown connects Armitage and Piwi in the cytosol to promote Piwi deposition to Yb bodies, before quickly returning to the cytosol. This return allows Armitage to transfer pre-Piwi-piRISC to the mitochondria for maturation. Shutdowns self-repulsion via its acidic N-terminus enables its transient residence in Yb bodies. A point mutation in Armitage, similar to a human Armitage/MOV10L1 mutation associated with azoospermia, traps Shutdown in Yb bodies, blocking Piwi-piRISC generation. This study reveals the mechanism of Shutdowns transient localization in Yb bodies and its essential role in Piwi-piRISC production and maintaining fertility.

molecular biology↗

bioRxiv2024

Aryl-hydrocarbon receptor in smooth muscle cells protect against dioxin induced adverse remodeling of atherosclerosis

IntroductionEnvironmental exposure to dioxin has been linked to increased myocardial infarction. Smooth muscle cells (SMC) in the coronary vasculature play a critical role in atherosclerotic plaque remodeling due to their phenotypic plasticity, however, the detailed mechanism linking dioxin exposure to adverse SMC modulation is not well understood. MethodsSingle-cell RNA and ATAC sequencing and histological analyses were performed on the aorta from mouse models of atherosclerosis exposed to 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) or control. Primary human coronary artery SMC (HCASMC) treated in culture with TCDD were used to perform RNA-Seq, ATAC-Seq, and functional phenotypic assays. ChIP-Seq was performed with antibodies against Aryl-hydrocarbon receptor (AHR) and TCF21, two of known SMC modulating transcription factors. ResultsModulated SMC were the most transcriptionally responsive cell type to dioxin in the atherosclerotic aorta. Dioxin accelerated disease phenotype by promoting a modulated SMC phenotype early, resulting in increased lesion size, migration of SMC, and macrophage recruitment to the lesion. We found C3 expressing modulated SMCs to be likely contributing to the increased macrophage recruitment and inflammation. Analysis of the RNA-Seq data from HCASMC treated with TCDD showed differential enrichment of biological pathways related to cell migration, localization, and inflammation. Furthermore, ATAC-Seq data showed a significant activation for pathways regulating vascular development, cell migration, inflammation, and apoptosis. With TCDD treatment, there was also enrichment of AHR ChIP-Seq peaks, while the TCF21 enrichment decreased significantly. The SMC-specific Ahr knockout resulted in increased oxidative stress in SMC, increased lesion size and macrophage content, and loss of SMC lineage cells in the lesion cap when exposed to TCDD, consistent with a more vulnerable plaque phenotype. ConclusionDioxin adversely remodels atherosclerotic plaque by accelerating the SMC- phenotypic modulation, and increasing inflammation and oxidative stress resulting in increased macrophage recruitment and lesion size. Dioxin may adversely affect the SMC phenotype and disease state by affecting the TCF21 occupancy in the open chromatin regions. Furthermore, we observed that SMC-specific deletion of Ahr in mice resulted in worsening of dioxin mediated SMC modulation and atherosclerosis, suggesting that Ahr in SMC confers protection against dioxin by promoting a stable plaque phenotype and reducing dioxin induced oxidative stress. SummaryO_LIExposure to dioxin, an environmental pollutant present in tobacco smoke and air pollution, accelerates smooth muscle cell modulation, and atherosclerosis. C_LIO_LIDioxin exposure leads to inflammatory smooth muscle cell phenotype characterized by complement pathway activation and increased macrophage recruitment to plaque C_LIO_LIAryl-hydrocarbon receptor in SMC protects against oxidative stress, and promotes a stable plaque phenotype C_LI

molecular biology↗

bioRxiv2023

Combination of differential expression and co-expression network analyses identify novel conserved age-associated changes among different tissues

Transcriptomic changes occur with age, but the extent of their similarities across tissues is not clear. Previous studies have identified no similarity in age-modulated genes in different tissues. In this study, we sought to identify transcriptional changes with age across tissues using differential network analysis, with the premise that differential expression analysis alone is not capable of detecting all the changes in the transcriptional landscape that occur in tissues with age. Our results show major transcriptional alterations not detected by differential expression analysis that can be detected by differential connectivity analysis. Combining these two analyses, we detected genes changing across tissues, enriched in "RNA splicing" and "RNA processing", and highly connected in protein-protein interaction networks. Co-expression module analyses demonstrated that other genes with tissue-specific variations with age are enriched in pathways that combat accumulation of aberrant RNAs and proteins, which are caused by defective splicing. Additionally, tissues displayed a major reorganization of their genes connectivities with age, with most demonstrating convergent connectivity patterns. Our analyses identify genes and processes which transcriptional changes are conserved across tissues, demonstrating a central role for RNA splicing and processing genes and highlighting the importance of differential network analysis for understanding the ageing transcriptome.

bioinformatics↗

bioRxiv2022

Convergent evolution in silico reveals shape and dynamic principles of directed locomotion

Active, directed locomotion on the ground is present in many phylogenetically distant species. Bilateral symmetry and modularity of the body are common traits often associated with improved directed locomotion. Nevertheless, both features result from natural selection, which is contingent (history-dependent) and multifactorial (several factors interact simultaneously). Based solely on the unique natural history on Earth, it is difficult to conclude that bilateral symmetry and modularity of the body are required traits for an improved locomotion ability as they can result from chance or be related to other body functions. As a way to avoid these caveats, we propose using physics-based simulations of 3D voxel-based soft robots evolved under different evolutionary scenarios to test the necessity of both traits for sustained and effective displacement on the ground. We found that an intermediate number of body modules (appendages) and high body symmetry are evolutionarily selected regardless of gravitational environments, robot sizes, and genotype encoding. Therefore, we conclude that both traits are strong candidates for universal principles related to improved directed locomotion.

evolutionary biology↗

bioRxiv2021

Cannabidiol activates neuronal Kv7 channels

Cannabidiol (CBD), a chemical found in the Cannabis sativa plant, is a clinically effective antiepileptic drug whose mechanism of action is unknown. Using a fluorescence-based thallium flux assay, we performed a large-scale screen and found enhancement of flux through heterologously-expressed human Kv7.2/7.3 channels by CBD. Using patch clamp recordings, we found that CBD at low concentrations activates Kv7.2/7.3 channels at subthreshold voltages, with 100 nM CBD producing a doubling of current at -50 mV. CBD shifted the voltage-dependence of channels in the hyperpolarizing direction, producing a shift in the midpoint of activation by [~]-14 mV at 300 nM. CBD also effectively enhanced native M-current in both mouse superior cervical ganglion neurons and rat hippocampal neurons. The potent enhancement of Kv2/7.3 channels by CBD seems likely to contribute to its effectiveness as an antiepileptic drug by reducing neuronal hyperexcitability.

neuroscience↗

bioRxiv2021

Liquid-liquid phase separation of florigen activation complex induces flowering

Floral transition, regulated by the systemic action of the mobile florigen protein FLOWERING LOCUS T (FT), is essential for successful plant reproduction1. How FT controls downstream gene expression remains incompletely understood, although it relies on the florigen activation complex (FAC), a core component of FT function2-4. The FAC is a nucleus-localized transcriptional activator of genes encoding MADS-box transcription factors critical to reproductive development and consists of florigen FT; a scaffold 14-3-3 protein that is a key component for complex assembly; and FD, a basic leucine-zipper protein that recruits the FAC to DNA. Here we report that the FAC exhibits phase separation. In rice shoot apical meristem cells, rice florigen Heading date 3a (Hd3a) fused to the green fluorescent protein formed speckles in the nucleus. The FAC speckle is formed in a FAC-dependent manner in tobacco cells. Recombinant Hd3a, but not OsFD1, phase-separated in vitro, and this effect was enhanced in the presence of 14-3-3 protein. Furthermore, mutations affecting functionally important residues in the pocket region or C-terminal disordered region of Hd3a affected FAC phase separation, providing a biochemical framework for the proteins effect on flowering. The ability to form condensates via phase transition represents a previously unknown mechanism for gene activation by the FAC.

plant biology↗

bioRxiv2019

Long-read sequencing identifies GGC repeat expansion in human-specific NOTCH2NLC associated with neuronal intranuclear inclusion disease

Neuronal intranuclear inclusion disease (NIID) is a progressive neurodegenerative disease characterized by eosinophilic hyaline intranuclear inclusions in neuronal and somatic cells. The wide range of clinical manifestations in NIID makes ante-mortem diagnosis difficult 1-8, but skin biopsy realized its ante-mortem diagnosis 9,10 and many NIID cases have been diagnosed by skin biopsy11,12. Most cases of NIID are sporadic, but several familial cases are known. Using a large NIID family, we conducted linkage mapping, found a 58.1-Mb linked-region at 1p22.1-q21.3 with a maximum logarithm of odds (LOD) score of 4.21, and successfully identified a GGC repeat expansion in the 5 portion of NOTCH2NLC in all affected members by long-read sequencing, but not in unaffected members. We further found the similar expansions in additional 8 unrelated families with NIID as well as 39 sporadic NIID patients. Repeat-primed PCR consistently detected the GGC repeat expansion in all the familial and sporadic patients diagnosed by skin biopsy, but never in unaffected family members nor 200 controls. This shows that pathogenic changes in a human-specific gene evolutionarily generated by segmental duplication indeed causes a human disease.

genetics↗