Biology subjects

Fukunaga, K.

Publications and source records attributed to Fukunaga, K..

11 recordsLinked to original sources

bioRxiv2026

A Competitive Fluorescence Immunoassay Based on Intermolecular Quenching Using an N-Terminally Fluorescent-Labeled IgG Antibody

The development of antibody-based fluorescent sensors relying on tryptophan-mediated quenching, such as Quenchbody (Q-body), often exhibits limited fluorescence responses because dye quenching depends on the location of tryptophan residues within the antibody. Here, we developed a competitive fluorescence immunoassay, termed an intermolecular Quenchbody (iQ-body), that utilizes intermolecular Forster resonance energy transfer (FRET) between an N-terminally fluorescent-labeled IgG antibody and an antigen-quencher conjugate. Anti-thyroxine IgG antibody (clone 6901 SPTN-5) showed minimal fluorescence changes upon antigen binding, despite N-terminal labeling with TAMRA. In contrast, the addition of an antigen-quencher conjugate (QSY9-T3) effectively quenched the TAMRA fluorescence via intermolecular FRET. Subsequent competitive displacement by thyroxine (T4) resulted in concentration-dependent fluorescence recovery. The iQ-body strategy provides a simple approach for constructing competitive fluorescence immunoassays for small-molecule targets using publicly available IgG antibodies.

biophysics↗

bioRxiv2025

Astrocytic FABP5 drives non-cell-autonomous oligodendrocyte injury in multiple system atrophy by promoting TNF signaling and ferroptotic stress

Multiple system atrophy (MSA) is a fatal -synucleinopathy characterized by progressive parkinsonism, cerebellar and autonomic dysfunction. Currently, the mechanisms driving cerebellar white matter neuroinflammation and degeneration in MSA are poorly understood. Here, we identified fatty acid-binding protein 5 (FABP5) as a key factor regulating cerebellar inflammation in MSA pathogenesis in a detailed study of human, mouse and cultured astrocytes. Firstly, transcriptomic profiling of human MSA cerebellar white matter revealed activation of pro-inflammatory and ferroptotic pathways, with FABP5 identified as a key pathway component that is upregulated. We confirmed that FABP5 is upregulated in reactive astrocytes in the PLP--syn transgenic mouse model, also in LPS-treated primary astrocytes. Fabp5 silencing suppressed TNF signaling, mitigated ferroptosis, and restored mitochondrial function. These findings suggest astrocytic FABP5 as a central intracellular regulator linking glial inflammation, ferroptosis, and mitochondrial injury. Overall, this mechanism suggests that FABP5 drives pathology mediated by astrocytes oligodendroglia in MSA, therefore representing a novel and promising therapeutic target.

neuroscience↗

bioRxiv2023

Quantification of the escape from X chromosome inactivation with the million cell-scale human single-cell omics datasets reveals heterogeneity of escape across cell types and tissues

One of the two X chromosomes of females is silenced through X chromosome inactivation (XCI) to compensate for the difference in the dosage between sexes. Among the X-linked genes, several genes escape from XCI, which could contribute to the differential gene expression between the sexes. However, the differences in the escape across cell types and tissues are still poorly characterized because no methods could directly evaluate the escape under a physiological condition at the cell-cluster resolution with versatile technology. Here, we developed a method, single-cell Level inactivated X chromosome mapping (scLinaX), which directly quantifies relative gene expression from the inactivated X chromosome with droplet-based single-cell RNA-sequencing (scRNA-seq) data. The scLinaX and differentially expressed genes analyses with the scRNA-seq datasets of [~]1,000,000 blood cells consistently identified the relatively strong degree of escape in lymphocytes compared to myeloid cells. An extension of scLinaX for multi-modal datasets, scLinaX-multi, suggested a stronger degree of escape in lymphocytes than myeloid cells at the chromatin-accessibility level with a 10X multiome dataset. The scLinaX analysis with the human multiple-organ scRNA-seq datasets also identified the relatively strong degree of escape from XCI in lymphoid tissues and lymphocytes. Finally, effect size comparisons of genome-wide association studies between sexes identified the larger effect sizes of the PRKX gene locus-lymphocyte counts association in females than males. This could suggest evidence of the underlying impact of escape on the genotype-phenotype association in humans. Overall, scLinaX and the quantified catalog of escape identified the heterogeneity of escape across cell types and tissues and would contribute to expanding the current understanding of the XCI, escape, and sex differences in gene regulation.

genomics↗

bioRxiv2022

Memory B cells and memory T cells induced by SARS-CoV-2 booster vaccination or infection show different dynamics and efficacy to the Omicron variant.

Although BNT162b2 vaccination was shown to prevent infection and reduce COVID-19 severity, and the persistence of immunological memory generated by the vaccination has not been well elucidated. We evaluated memory B and T cell responses to the SARS-CoV-2 spike protein before and after the third BNT162b2 booster. Although the antibody titer against the spike receptor-binding domain (RBD) decreased significantly 8 months after the second vaccination, the number of memory B cells continued to increase, while the number of memory T cells decreased slowly. Memory B and T cells from unvaccinated infected patients showed similar kinetics. After the third vaccination, the antibody titer increased to the level of the second vaccination, and memory B cells increased at significantly higher levels before the booster, while memory T cells recovered close to the second vaccination levels. In memory T cells, the frequency of CXCR5+CXCR3+CCR6- cTfh1 was positively correlated with RBD-specific antibody-secreting B cells. Furthermore, T cell-dependent antibody production from reactivated memory B cells in vitro was correlated to the Tfh-like cytokine levels. For the response to variant RBDs, although 60%-80% of memory B cells could bind to the Omicron RBD, their binding affinity was low, while memory T cells show an equal response to the Omicron spike. Thus, the persistent presence of memory B and T cells will quickly upregulate antibody production and T cell responses after Omicron strain infection, which prevents severe illness and death due to COVID-19.

immunology↗

bioRxiv2022

Fc-modified SARS-CoV-2 neutralizing antibodies with therapeutic effects in two animal models.

The use of therapeutic neutralizing antibodies against SARS-CoV-2 infection has been highly effective. However, there remain few practical antibodies against viruses that are acquiring mutations. In this study, we created 494 monoclonal antibodies from COVID-19-convalescent patients, and identified antibodies that exhibited comparable neutralizing ability to clinically used antibodies in the neutralization assay using pseudovirus and authentic virus including variants of concerns. These antibodies have different profiles against various mutations, which were confirmed by cell-based assay and cryo-electron microscopy. To prevent antibody-dependent enhancement, N297A modification was introduced, and showed a reduction of lung viral RNAs by therapeutic administration in a hamster model. In addition, an antibody cocktail consisting of three antibodies was also administered therapeutically to a macaque model, which resulted in reduced viral titers of swabs and lungs and reduced lung tissue damage scores. These results showed that our antibodies have sufficient antiviral activity as therapeutic candidates.

microbiology↗

bioRxiv2022

Epsin2, a novel target for multiple system atrophy therapy via regulating α-synuclein propagation associated with FABP7

Multiple system atrophy (MSA) is a neurodegenerative disease showing accumulation of misfolded -synuclein and myelin disruption. However, the mechanism how -synuclein (-syn) accumulate in MSA brain remains unclear. Here, we identify the protein epsin-2 as a novel target for MSA therapy via controlling -synuclein accumulation. In MSA mouse model, PLP-hSyn transgenic mice and FABP7/-syn hetero-aggregates injected mice, we firstly found that fatty acid-binding protein 7 (FABP7) related to MSA development and formed hetero-aggregates with -syn, which exhibited stronger toxicity than -syn aggregates. Furthermore, injected FABP7/-syn hetero-aggregates in mice selectively accumulated in oligodendrocytes and Purkinje neurons and cause cerebellar dysfunction. By bioinformatic analyses, the protein epsin-2 expresses in both oligodendrocyte and Purkinje cells was found as a potential target to regulate FABP7/-syn hetero-aggregates propagation via clathrin-dependent endocytosis. The AAV5-dependent epsin-2 knock-down mice exhibited decreased levels of aggregates accumulation in Purkinje neurons and oligodendrocytes as well as performed improved myelin levels and Purkinje neurons in cerebellum and motor functions. Thus, we propose epsin-2 as a novel and therapeutic candidate for MSA.

pathology↗

bioRxiv2022

Quantitative live-cell imaging of secretion activity reveals dynamic immune responses

The measurement of cytokine secretions has contributed to the development of immunology; however, new methods that enable highly sensitive and efficient analysis are required for the precise characterisation of dynamic secretion activity when using rare cells or limited human specimens. Here, we report a new technology for quantitative live-cell imaging of secretion activity (qLCI-S), that enables high-throughput and dual-colour detection of prolonged secretion activity at the single-cell level, followed by transcriptome analysis for individual cells based on their phenotype. The power of the qLCI-S was demonstrated by visualising the individual and longitudinal cytokine secretion patterns of group 2 innate lymphoid cells, which comprised <0.01% human peripheral blood mononuclear cells, and identifying their minor subpopulations. This new technology will provide new insights into the spatiotemporal dynamic nature of various secretory functions and the development of fundamental tools for phenotypic drug discovery and regenerative and precision medicine.

biophysics↗

bioRxiv2021

Nasal delivery of single-domain antibodies improve symptoms of SARS-CoV-2 infection in an animal model

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes the disease COVID-19 can lead to serious symptoms, such as severe pneumonia, in the elderly and those with underlying medical conditions. While vaccines are now available, they do not work for everyone and therapeutic drugs are still needed particularly for treating life-threatening conditions. Here, we showed nasal delivery of a new, unmodified camelid single-domain antibody (VHH), termed K-874A, effectively inhibited SARS-CoV-2 titers in infected lungs of Syrian hamsters without causing weight loss and cytokine induction. In vitro studies demonstrated that K-874A neutralized SARS-CoV-2 in both VeroE6/TMPRSS2 and human lung-derived alveolar organoid cells. Unlike other drug candidates, K-874A blocks viral membrane fusion rather than viral attachment. Cryo-electron microscopy revealed K-874A bound between the receptor binding domain and N-terminal domain of the virus S protein. Further, infected cells treated with K-874A produced fewer virus progeny that were less infective. We propose that direct administration of K-874A to the lung via a nebulizer could be a new treatment for preventing the reinfection of amplified virus in COVID-19 patients. Author summaryVaccines for COVID-19 are now available but therapeutic drugs are still needed to treat life-threatening cases and those who cannot be vaccinated. We discovered a new heavy-chain single-domain antibody that can effectively neutralize the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes COVID-19. Unlike other drug candidates, which prevent the virus from attaching to the receptor on the host cell, this new antibody acts by blocking the virus membrane from fusing with the host cell membrane. We studied the behavior of the new antibody in vitro using VeroE6/TMPRSS2 cells and human lung organoids. When delivered through the nose to infected Syrian hamsters, we found that this antibody could prevent the typical symptoms caused by SARS-CoV-2. Our results are significant because delivering simple drugs directly to infected lungs using a nebulizer could increase the potency of the drugs while reducing the risk of immune reaction that could occur if the drugs escape or are delivered through the blood stream.

microbiology↗

bioRxiv2019

Enhanced emotional memory retrieval by chemogenetic activation of locus coeruleus norepinephrine neurons

The ability to retrieve memory store in response to the environment is essential for animal behavioral adaptation. Norepinephrine (NE)-containing neurons in the brain play a key role in the modulation of synaptic plasticity underlying various processes of memory formation. However, the role of the central NE system in memory retrieval remains unclear. In this study, we developed a neural chemogenetic activation strategy using insect olfactory Ionotropic Receptors (IRs), and used it for selective stimulation of NE neurons in the locus coeruleus (LC) in transgenic mice. Ligand-induced activation of LC NE neurons resulted in enhancement of the retrieval process of conditioned taste aversion, which was mediated through at least partly adrenergic receptors in the amygdala. Pharmacological blockade of LC activity confirmed the facilitative role of these neurons in memory retrieval. Our findings indicate that the LC-amygdalar pathway is required and sufficient for enhancing the recall of taste associative memory.

neuroscience↗

bioRxiv2019

Relationship between ocean area and incidence of anthropogenic debris ingested by longnose lancetfish (Alepisaurus ferox)

Longnose lancetfish (Alepisaurus ferox) may has been studied as an indicator of marine pollution caused by marine litter. The objectives of this study were to determine the difference in frequency of occurrence of plastics ingested by longnose lancetfish in different ocean area. In this study, we compared the incidence and characteristics of anthropogenic debris in the stomachs of longnose lancetfish. We examined 91 longnose lancetfish caught by pelagic longline fishing in Sagami Bay, the North Pacific Ocean, approximately 200 km south of Shikoku, and in the Indian Ocean. Broken down by ocean area, the incidence of anthropogenic debris ingestion was highest in Sagami Bay (23 of 34 specimens, 68%), followed by the North Pacific Ocean (1 of 9, 11%), and the Indian Ocean (8 of 48, 17%). The frequency of occurrence increased in area close to the sphere of human habitation. The anthropogenic debris collected in this study were more than 70% classified as plastic sheeting. Stomach content analysis revealed that more than 90% of the plastic fragments were composed of PP and PE, which have specific gravities that are less than that of seawater. The results of this study show that some of the plastics flowing from the land into the sea are spreading through under the water surface of the ocean.

ecology↗

bioRxiv2018

Laminin heparin-binding peptides promiscuously bind growth factors and enhance diabetic wound healing

Laminin, as a key component of the basement membrane extracellular matrix (ECM), regulates tissue morphogenesis. We show that multiple laminin isoforms promiscuously bind to growth factors (GFs) with high affinity, through their heparin binding domains (HBDs) located in the a chain LG domains. Interestingly, these domains also bind to syndecan cell-surface receptors, promoting attachment of fibroblasts and endothelial cells. We next explore application of these multifunctional laminin HBDs in skin healing in the type 2 diabetic mouse. We demonstrate that covalent incorporation of laminin HBDs into fibrin matrix enables the slow-release of GFs. Incorporation of the 33043-3067 laminin HBD significantly enhances in vivo wound-healing efficacy of vascular endothelial cell growth factor (VEGF)-A165 and platelet-derived growth factor (PDGF)-BB, under conditions where the GFs alone in fibrin are inefficacious. This laminin HBD peptide may be clinically useful by improving biomaterials as both GF reservoirs and cell scaffolds, leading to effective tissue regeneration.

bioengineering↗