Biology subjects

Okada, M.

Publications and source records attributed to Okada, M..

At least 37 records · Page 2Linked to original sources

bioRxiv2023

An engineered ACE2 decoy broadly neutralizes Omicron subvariants and shows therapeutic effect in SARS-CoV-2-infected cynomolgus macaques

The Omicron variant continuously evolves under the humoral immune pressure obtained by vaccination and SARS-CoV-2 infection and the resultant Omicron subvariants exhibit further immune evasion and antibody escape. Engineered ACE2 decoy composed of high-affinity ACE2 and IgG1 Fc domain is an alternative modality to neutralize SARS-CoV-2 and we previously reported its broad spectrum and therapeutic potential in rodent models. Here, we show that engineered ACE2 decoy retains the neutralization activity against Omicron subvariants including the currently emerging XBB and BQ.1 which completely evade antibodies in clinical use. The culture of SARS-CoV-2 under suboptimal concentration of neutralizing drugs generated SARS-CoV-2 mutants escaping wild-type ACE2 decoy and monoclonal antibodies, whereas no escape mutant emerged against engineered ACE2 decoy. As the efficient drug delivery to respiratory tract infection of SARS-CoV-2, inhalation of aerosolized decoy treated mice infected with SARS-CoV-2 at a 20-fold lower dose than the intravenous administration. Finally, engineered ACE2 decoy exhibited the therapeutic efficacy for COVID-19 in cynomolgus macaques. Collectively, these results indicate that engineered ACE2 decoy is the promising therapeutic strategy to overcome immune-evading SARS-CoV-2 variants and that liquid aerosol inhalation can be considered as a non-invasive approach to enhance efficacy in the treatment of COVID-19.

microbiology↗

bioRxiv2022

A novel TGF-β-responsive enhancer regulates SRC expression and epithelial-mesenchymal transition-associated cell migration

The non-receptor tyrosine kinase SRC is overexpressed and/or hyperactivated in various human cancers, and facilitates cancer progression by promoting invasion and metastasis. However, the mechanisms underlying SRC upregulation are poorly understood. In this study, we demonstrated that transforming growth factor-{beta} (TGF-{beta}) induces SRC expression at the transcriptional level by activating a novel intragenic SRC enhancer. In the human breast epithelial cell line MCF10A, TGF-{beta}1 stimulation upregulated the SRC1A promoter, resulting in increased SRC mRNA and protein levels. Chromatin immunoprecipitation (ChIP)-sequencing analysis revealed that SMAD complex is recruited to three enhancer regions ~15 kb upstream and downstream of the SRC promoter, and one of them is capable of activating the SRC promoter in response to TGF-{beta}. In addition, JUN, which is a member of the activator protein (AP)-1 family, also localizes to the enhancer and regulates TGF-{beta}-induced SRC expression. Furthermore, the total amount of active SRC also increased, coinciding with the TGF-{beta}-induced SRC expression. In TGF-{beta}-induced epithelial-mesenchymal transition (EMT), TGF-{beta}-induced SRC upregulation plays a crucial role in EMT-associated cell migration by activating the SRC/focal adhesion kinase (FAK) circuit. Overall, these results suggest that TGF-{beta}-induced SRC upregulation promotes cancer cell invasion and metastasis in a subset of human malignancies.

molecular biology↗

bioRxiv2022

SARS-CoV-2 ORF8 is a viral cytokine regulating immune responses

Many patients with severe COVID-19 suffer from pneumonia, and thus elucidation of the mechanisms underlying the development of such severe pneumonia is important. The ORF8 protein is a secreted protein of SARS-CoV-2, whose in vivo function is not well understood. Here, we analyzed the function of ORF8 protein by generating ORF8-knockout SARS-CoV-2. We found that the lung inflammation observed in wild-type SARS-CoV-2-infected hamsters was decreased in ORF8-knockout SARS-CoV-2-infected hamsters. Administration of recombinant ORF8 protein to hamsters also induced lymphocyte infiltration into the lungs. Similar pro-inflammatory cytokine production was observed in primary human monocytes treated with recombinant ORF8 protein. Furthermore, we demonstrate that the serum ORF8 protein levels are correlated well with clinical markers of inflammation. These results demonstrated that the ORF8 protein is a viral cytokine of SARS-CoV-2 involved in the in the immune dysregulation observed in COVID-19 patients, and that the ORF8 protein could be a novel therapeutic target in severe COVID-19 patients.

microbiology↗

bioRxiv2022

Landscape of infection enhancing antibodies in COVID-19 and healthy donors

To assess the frequency of SARS-CoV-2 infection enhancing antibodies in the general population, we searched over 64 million heavy chain antibody sequences from healthy and COVID-19 patient repertoires for sequences similar to 11 previously reported enhancing antibodies. Although the distribution of sequence identities was similar in COVID-19 and healthy repertoires, the COVID-19 hits were significantly more clonally expanded than healthy hits. Furthermore, among the tested hits, 17 out of 94 from COVID-19, compared with 2 out of 96 from healthy, bound to the enhancing epitope. A total of 6 of the 19 epitope-binding antibodies enhanced ACE2 receptor binding to the spike protein. Together, this study revealed that enhancing antibodies are far more frequent in COVID-19 patients than in healthy donors, but a reservoir of potential enhancing antibodies exists in healthy donors that could potentially mature to actual enhancing antibodies upon infection.

immunology↗

bioRxiv2022

Sugar chain structure of apolipoprotein B-100 and its role in oxidation

The aim of this research was to determine the structure of oligosaccharide antennae located on the surface of apoB-100, and to examine their roles in the oxidation process and in the signal transduction of endothelial cells. The profiles of oligosaccharides on apoB-100 were determined by enzymatic digestions as follows. First, N-glycanase was used to release a mixture of oligomannose and complex types of oligosaccharides. Second, endoglycosidase H was used to release high-mannose and hybrid types. Third, O-glycosidase DS was used to release O-linked oligosaccharides. The released oligosaccharides were then labeled and quantified by electrophoresis. In vitro apoB-100 oxidation was mimicked by adding transition copper ions. For the signal transduction study, I examined the expression of adhesion molecules on cultured human coronary artery endothelial cells by adding LDL in which the oligosaccharide sequences were enzymatically modified. The sugar chain structures on the surface part of apoB-100 were composed predominantly of N-linked oligosaccharides, i.e., two forms of complex type and five forms of high-mannose type. The digestion of sugar chains by exoglycosidases and endoglycosidases did not result in any changes in the susceptibility of LDL to oxidation. Also, LDL without monosaccharides such as sialic acid, galactose, and N-acetylglucosamine did not induce any significant effect on the expression of ICAM-1, VCAM-1, or ELAM-1. I found that the sugar chains did not play any significant roles in the oxidative processing of LDL and also in the expression of ICAM-1, VCAM-1, or ELAM-1.

biochemistry↗

bioRxiv2022

Modeling Pulse Dynamics of Juvenile Fish Enables the Short-term Forecasting of Population Dynamics in Japanese Pufferfish: A Latent Variable Approach

The time lag between data collection and management implementation is a source of uncertainty and bias in the calculation of acceptable biological catch. Here, we developed a method to use small-scale survey data for juvenile Japanese pufferfish (Takifugu rubripes) to shorten this time lag and achieve accurate short-term forecasting. A survey of juvenile fish at a local sandy beach in Ise-Mikawa Bay, Japan provides data for the strength of year classes before fisheries recruitment; however, it is difficult to use the raw data owing to the small sample size and large observation errors. We found that a random-effect model overcame these problems and more accurately predicted pulse patterns of catch rates to derive a standardized recruitment index compared with a fixed-effect model. We then showed that a stock assessment model using the standardized recruitment index from the random-effect model outperformed models without the standardized recruitment index with respect to retrospective forecasting ability. This study highlights the applicability of a latent-variable approach for standardizing small-scale survey data and thereby for unbiased forecasting of short-term fish dynamics.

ecology↗

bioRxiv2021

Distinct and interchangeable growing patterns in colorectal cancer stem-like cells are regulated by Musashi-1

The dynamic and heterogeneous features of cancer stem-like cells (CSCs) have been widely recognized, but their nongenetic cellular plasticity mechanisms remain elusive. By using colorectal cancer organoids, we phenotypically tracked their spheroid formation and growth capacity to a single-cell resolution, and we discovered that the spheroid-forming cells exhibit a heterogeneous growth pattern, consisting of slow- and fast-growing spheroids. The isolated fast-growing spheroids seem to preserve a dual-growing pattern through multiple passages, whereas the isolated slow-growing spheroids are restricted to a slow-growing pattern. Notably, the spheroids of both patterns were tumorigenic. Moreover, the expression of CSC markers varied among the subpopulations with different growth patterns. The isolated slow-growing spheroids adopted the dual-growing pattern by various extrinsic triggers, in which Musashi-1 plays a key role. The slow-growing fraction was resistant to chemotherapy, and its successful isolation can provide an in vitro platform allowing us to elucidate their role in drug resistance.

cancer biology↗

bioRxiv2021

The SARS-CoV-2 Delta variant is poised to acquire complete resistance to wild-type spike vaccines

mRNA-based vaccines provide effective protection against most common SARS-CoV-2 variants. However, identifying likely breakthrough variants is critical for future vaccine development. Here, we found that the Delta variant completely escaped from anti-N-terminal domain (NTD) neutralizing antibodies, while increasing responsiveness to anti-NTD infectivity-enhancing antibodies. Although Pfizer-BioNTech BNT162b2-immune sera neutralized the Delta variant, when four common mutations were introduced into the receptor binding domain (RBD) of the Delta variant (Delta 4+), some BNT162b2-immune sera lost neutralizing activity and enhanced the infectivity. Unique mutations in the Delta NTD were involved in the enhanced infectivity by the BNT162b2-immune sera. Sera of mice immunized by Delta spike, but not wild-type spike, consistently neutralized the Delta 4+ variant without enhancing infectivity. Given the fact that a Delta variant with three similar RBD mutations has already emerged according to the GISAID database, it is necessary to develop vaccines that protect against such complete breakthrough variants.

microbiology↗

bioRxiv2021

Critical Role for Isoprenoids in Apicoplast Biogenesis by Malaria Parasites

Isopentenyl pyrophosphate (IPP) is an essential metabolic output of the apicoplast organelle in Plasmodium falciparum malaria parasites and is required for prenylation-dependent vesicular trafficking and other cellular processes. We have elucidated a critical and previously uncharacterized role for IPP in apicoplast biogenesis. Inhibiting IPP synthesis blocks apicoplast elongation and inheritance by daughter merozoites, and apicoplast biogenesis is rescued by exogenous IPP and polyprenols. Knockout of the only known isoprenoid-dependent apicoplast pathway, tRNA prenylation by MiaA, has no effect on blood-stage parasites and thus cannot explain apicoplast reliance on IPP. However, we have localized an annotated polyprenyl synthase (PPS) to the apicoplast lumen. PPS knockdown is lethal to parasites, rescued by IPP, and blocks apicoplast biogenesis, thus explaining apicoplast dependence on isoprenoid synthesis. We hypothesize that PPS synthesizes long-chain polyprenols critical for apicoplast membrane fluidity and biogenesis. This work critically expands the paradigm for isoprenoid utilization in malaria parasites and identifies a novel essential branch of apicoplast metabolism suitable for therapeutic targeting.

microbiology↗

bioRxiv2021

Imaging and single cell sequencing analyses of super-enhancer activation mediated by NF-κB in B cells

The transcription factor NF-{kappa}B, which plays an important role in cell fate determination, is involved in the activation of super-enhancers (SEs). However, the biological functions of the NF-{kappa}B SEs in gene control are not fully elucidated. We investigated the characteristics of NF-{kappa}B-mediated SE activity using fluorescence live-cell imaging of RelA, single-cell transcriptome, and chromatin accessibility analyses in anti-IgM-stimulated B cells. Cell stimulation induced nuclear foci formation of RelA and gene expression in a switch-like manner. The gained SEs induced a higher fold-change expression and enhanced cell-to-cell variability in transcriptional response. These properties were correlated with the number of gained cis-regulatory interactions, while switch-like gene induction was associated with the number of NF-{kappa}B binding sites in SE. Our study suggests that NF-{kappa}B SEs have unique roles for quantitative control of gene expression through direct binding to accessible DNA and enhanced DNA contacts.

molecular biology↗

bioRxiv2021

Functional annotation-driven unsupervised clustering of single-cell transcriptomes

MotivationSingle-cell RNA sequencing (scRNA-seq) analysis reveals heterogeneity and dynamic cell transitions. However, conventional gene-based analyses require intensive manual curation to interpret the biological implications of computational results. Hence, a theory for efficiently annotating individual cells is necessary. ResultsWe present ASURAT, a computational pipeline for simultaneously performing unsupervised clustering and functional annotation of disease, cell type, biological process, and signaling pathway activity for single-cell transcriptomic data, using correlation graph-based decomposition of genes based on database-derived functional terms. We validated the usability and clustering performance of ASURAT using scRNA-seq datasets for human peripheral blood mononuclear cells, which required fewer manual curations than existing methods. Moreover, we applied ASURAT to scRNA-seq and spatial transcriptome datasets for small cell lung cancer and pancreatic ductal adenocarcinoma, identifying previously overlooked subpopulations and differentially expressed genes. ASURAT is a powerful tool for dissecting cell subpopulations and improving biological interpretability of complex and noisy transcriptomic data. AvailabilityA GPLv3-licensed implementation of ASURAT is on GitHub (https://github.com/keita-iida/ASURAT).

bioinformatics↗

bioRxiv2021

Src activation in lipid rafts confers epithelial cells with invasive potential to escape from apical extrusion during cell competition

Abnormal/cancerous cells within healthy epithelial tissues undergo apical extrusion to protect against carcinogenesis, while they acquire invasive capacity once carcinogenesis progresses. However, the molecular mechanisms by which cancer cells escape from apical extrusion and invade surrounding tissues remain elusive. We found that during competition within epithelial cell layers, Src-transformed cells underwent basal delamination by Src activation within lipid rafts, whereas they were apically extruded when Src was outside of lipid rafts. Comparative analysis of contrasting phenotypes revealed that activation of the Src-STAT3-MMP axis through lipid rafts was required for basal delamination. CUB domain-containing protein 1 (CDCP1) was identified as an Src activating scaffold in lipid rafts, and its overexpression induced basal delamination. In renal cancer spheroids, CDCP1 promoted HGF-dependent invasion by activating the Src-STAT3-MMP axis. Overall, these results suggest that Src activation in lipid raft confers resistance to apical extrusion and invasive potential on epithelial cells to promote carcinogenesis.

cell biology↗

bioRxiv2021

Multi-state structure determination and dynamics analysis reveals a new ubiquitin-recognition mechanism in yeast ubiquitin C-terminal hydrolase

Despite accumulating evidence that protein dynamics is indispensable for understanding the structural basis of biological activities, it remains challenging to visualize the spatial description of the dynamics and to associate transient conformations with their molecular functions. We have developed a new NMR protein structure determination method for the inference of multi-state conformations using multiple types of NMR data, including paramagnetic NMR and residual dipolar couplings, as well as conventional NOEs. Integration of these data in the structure calculation permits delineating accurate ensemble structures of biomacromolecules. Applying the method to the protein yeast ubiquitin hydrolase 1 (YUH1), we find large dynamics of its N-terminus and crossover loop surrounding the active site for ubiquitin-recognition and proteolysis. The N-terminus gets into and out of the crossover loop, suggesting their underlying functional significance. Our results, including those from biochemical analysis, show that large motion surrounding the active site contributes strongly to the efficiency of the enzymatic activity.

biophysics↗

bioRxiv2020

An infectivity-enhancing site on the SARS-CoV-2 spike protein is targeted by COVID-19 patient antibodies

SARS-CoV-2 infection causes severe symptoms in a subset of patients, suggesting the presence of certain unknown risk factors. Although antibodies against the receptor-binding domain (RBD) of the SARS-CoV-2 spike have been shown prevent SARS-CoV-2 infection, the effects of antibodies against other spike protein domains are largely unknown. Here, we screened a series of anti-spike monoclonal antibodies from COVID-19 patients, and found that some of antibodies against the N-terminal domain (NTD) dramatically enhanced the binding capacity of the spike protein to ACE2, and thus increased SARS-CoV2 infectivity. Surprisingly, mutational analysis revealed that all the infectivity-enhancing antibodies recognized a specific site on the surface of the NTD. The antibodies against this infectivity-enhancing site were detected in all samples of hospitalized COVID-19 patients in the study. However, the ratio of infectivity-enhancing antibodies to neutralizing antibodies differed among patients. Furthermore, the antibodies against the infectivity-enhancing site were detected in 3 out of 48 uninfected donors, albeit at low levels. These findings suggest that the production of antibodies against SARS-CoV-2 infectivity-enhancing site could be considered as a possible exacerbating factors for COVID-19 and that a spike protein lacking such antibody epitopes may be required for safe vaccine development, especially for individuals with pre-existing enhancing antibodies.

microbiology↗

bioRxiv2020

Semisupervised definition of hippocampal ripples

Hippocampal ripples are transient neuronal features observed in high-frequency oscillatory bands of local field potentials, and they occur primarily during periods of behavioral immobility and slow-wave sleep. Ripples have been defined based on mathematically engineered features, such as magnitudes, durations, and cycles per event. However, the "ripples" could vary from laboratory to laboratory because their definition is subject to human bias, including the arbitrary choice of parameters and thresholds. In addition, local field potentials are often influenced by myoelectric noise arising from animal movement, making it difficult to distinguish ripples from high-frequency noises. To overcome these problems, we extracted ripple candidates under few constraints and labeled them as binary or stochastic "true" or "false" ripples using Gaussian mixed model clustering and a deep convolutional neural network in a weakly supervised fashion. Our automatic method separated ripples and myoelectric noise and was able to detect ripples even when the animals were moving. Moreover, we confirmed that a convolutional neural network was able to detect ripples defined by our method. Leave-one-animal-out cross-validation estimated the area under the precision-recall curve for ripple detection to be 0.72. Finally, our model establishes an appropriate threshold for the ripple magnitude in the case of the conventional detection of ripples.

neuroscience↗

bioRxiv2020

APC mutant cells exploit compensatory chromosome alterations to restore tumour cell fitness

Cancer cells tolerate copy number alterations (CNAs) of genomic regions that are lethal to non-cancer cells. Certain CNAs are preferentially associated with specific cancer types and lineages, but the mechanisms underlying the emergence and selection of specific CNAs remain unclear. Adenomatous polyposis coli (APC) mutations induce mitotic errors, but their impact on tumor evolution remains elusive. We investigated APC function in cultured cells and tumors and found that its loss led to {beta}-catenin accumulation at centrosomes, suppressing its maturation through inhibition of key centrosome regulators, including Aurora kinase A (AURKA) that promotes tumor growth. These defects collectively reduced cellular fitness, leading to impaired mitotic fidelity and delayed cell cycle progression. However, in APC-mutant tumors, AURKA activity was maintained, at least in part, through the amplification of chromosomes harboring AURKA and its activator genes, yet this alone was insufficient to fully restore proliferation: aberrant chromosomal reorganization also emerged and contributed to the adaptive fitness of APC-mutant cells. Such a process of adaptive CNA selection provides a framework for understanding how specific CNAs are selected to counteract disadvantages imposed by genetic alterations during tumor progression, providing one key insight into how specific CNAs are selected in this context.

cell biology↗

bioRxiv2020

Doxycycline has Distinct Apicoplast-Specific Mechanisms of Antimalarial Activity

Doxycycline (DOX) is a key antimalarial drug thought to kill Plasmodium parasites by blocking protein translation in the essential apicoplast organelle. Clinical use is primarily limited to prophylaxis due to delayed second-cycle parasite death at 1-3 M serum concentrations. DOX concentrations >5 M kill parasites with first-cycle activity but have been ascribed to off-target mechanisms outside the apicoplast. We report that 10 M DOX blocks apicoplast biogenesis in the first cycle and is rescued by isopentenyl pyrophosphate, an essential apicoplast product, confirming an apicoplast-specific mechanism. Exogenous iron rescues parasites and apicoplast biogenesis from first-but not second-cycle effects of 10 M DOX, revealing that first-cycle activity involves a metal-dependent mechanism distinct from the delayed-death mechanism. These results critically expand the paradigm for understanding the fundamental antiparasitic mechanisms of DOX and suggest repurposing DOX as a faster-acting antimalarial at higher dosing whose multiple mechanisms would be expected to limit parasite resistance.

microbiology↗

bioRxiv2020

Genetically targeted reporter imaging of deep neuronal network in the mammalian brain

Positron Emission Tomography (PET) allows biomolecular tracking, while PET monitoring of brain networks has been hampered by the lack of a suitable reporter. Here, we describe in vivo brain imaging that takes advantage of bacterial dihydrofolate reductase, ecDHFR, and its unique antagonist, TMP. In mice, peripheral administration of radiofluorinated and fluorescent TMP analogs enabled PET and intravital microscopy, respectively, of neuronal ecDHFR expressions. This technique is applicable to the visualization of neuronal ensemble activities elicited by chemogenetic manipulation in the mouse hippocampus. Notably, ecDHFR-PET offers mapping of neuronal projections in non-human primate brains, indicating the availability of ecDHFR-based tracking technologies for network monitoring. Finally, we demonstrate the utility of TMP analogs for PET assays of turnover and self-assembly of proteins tagged with ecDHFR mutants. Our findings may facilitate a broad spectrum of PET analyses of a mammalian brain circuit at molecular levels that were not previously applicable for technical reasons.

neuroscience↗