Biology subjects

Yamasaki, S.

Publications and source records attributed to Yamasaki, S..

At least 19 recordsLinked to original sources

bioRxiv2025

A lipid-driven, microbe-independent mechanism of acne via Lrig1+ follicular progenitor cells

Long-chain saturated fatty acids (lcSFAs) are abundant in the skin, but their pathogenic roles in acne remain unclear. In human sebum profiling, C16:0, the most abundant lcSFA, was the only fatty acid significantly elevated in acne and correlated with inflammatory comedone counts. We then established a mouse model that faithfully recapitulates human acne phenotypes, in which topical C16:0 penetrated the epidermis and induced sebocyte hyperplasia, comedogenesis, and follicular inflammation. Mechanistically, C16:0 activated keratinization and inflammatory pathways and drove sebocyte-lineage differentiation from Lrig1+progenitor cells, which function as cutaneous lipid sensors. These effects persisted in germ-free mice and were unaffected by fatty acid transporter modulation, while MyD88 signaling was partially required for inflammatory cell recruitment. Together, our findings identified C16:0 as a human acne-associated lipid that recapitulates disease hallmarks through a microbe-independent, lipid-driven pathway, highlighting Lrig1+cells as central hubs in remodeling of the pilosebaceous unit.

cell biology↗

bioRxiv2025

The antigen presenting molecule MR1 binds riboflavin catabolites

Major histocompatibility-complex (MHC) class I-related (MR1) protein presents vitamin B based antigens to Mucosal-Associated Invariant T (MAIT) cells. While microbial riboflavin precursors are well documented MR1 ligands, it is unclear whether host-generated riboflavin catabolites influence MR1-mediated immunity. Here, we report that riboflavin catabolites, including 10-formylmethylflavin (FMF), lumichrome, lumiflavin and alloxazine bind to MR1 with moderate affinity, while riboflavin itself binds weakly. In contrast to the microbial riboflavin antigens which increase MR1 cell surface expression, the riboflavin catabolites moderately reduced cell surface levels of MR1 by stabilizing and retaining MR1 in the endoplasmic reticulum (ER). The riboflavin catabolites appeared to bind to the intracellular MR1 and inhibit MR1 exit from the ER. These riboflavin catabolites also weakly competed with Vit B based Ags for MR1 binding, thereby inhibiting MAIT cell activation. The crystal structures of MR1 complexed with riboflavin, FMF, lumichrome and lumiflavin, show binding of these three-ringed ligands in the A-pocket of MR1. The crystal structure of MR1-lumichrome revealed that lumichrome formed a covalent "flavin bond" with MR1-Lys43 differing from the typical Schiff-base bond of MR1-Lys43-Ag complexes. Collectively, we identified three ring isoalloxazines that can bind MR1 and downregulate cell surface expression levels, suggesting a potential role in dampening MAIT cell immunity.

biochemistry↗

bioRxiv2024

The presenting HLA determines fidelity of SARS-CoV-2 spike protein epitope prediction

During the course of the COVID-19 pandemic, multiple studies used prediction methods to identify potential epitopes. While additional studies identified epitopes from convalescent and vaccinated subjects, few studies have compared the predicted to identified epitopes. Here we used three methods alone and in combination to predict helper T cell epitopes and compared the results to experimentally determined peptide binding. The correspondence between the results predicted from each method or combination and experimental results depends on the HLA being investigated. We were also able identify the prediction methods which lead to the most consistent results. Lastly, these observations were extended to more HLAs to predict epitopes which may be globally presented. All the predicted epitopes were previously identified as helper T cell epitopes. These results suggest predicting the binding to a larger number of HLAs may lead to higher fidelity identification of epitopes.

immunology↗

bioRxiv2023

Basement membrane extract potentiates the endochondral ossification phenotype of bone marrow-derived mesenchymal stem cell-based cartilage organoids

Endochondral ossification is a developmental process in the skeletal system and bone marrow of vertebrates. During endochondral ossification, primitive cartilaginous anlages derived from mesenchymal stem cells (MSCs) undergo vascular invasion and ossification. In vitro regeneration of endochondral ossification is beneficial for research on the skeletal system and bone marrow development as well as their clinical aspects. However, to achieve the regeneration of endochondral ossification, a stem cell-based artificial cartilage (cartilage organoid, Cart-Org) that possesses an endochondral ossification phenotype is required. Here, we modified a conventional 3D culture method to create stem cell-based Cart-Org by mixing it with a basement membrane extract (BME) and further characterized its chondrogenic and ossification properties. BME enlarged and matured the bone marrow MSC-based Cart-Orgs without any shape abnormalities. Histological analysis using Alcian blue staining showed that the production of cartilaginous extracellular matrices was enhanced in Cart-Org treated with BME. Transcriptome analysis using RNA sequencing revealed that BME altered the gene expression pattern of Cart-Org to a dominant chondrogenic state. BME triggered the activation of the SMAD pathway and inhibition of the NK-{kappa}B pathway, which resulted in the upregulation of SOX9, COL2A1, and ACAN in Cart-Org. BME also facilitated the upregulation of genes associated with hypertrophic chondrocytes (IHH, PTH1R, and COL10A1) and ossification (SP7, ALPL, and MMP13). Our findings indicate that BME promotes cartilaginous maturation and further ossification of bone marrow MSC-based Cart-Org, suggesting that Cart-Org treated with BME possesses the phenotype of endochondral ossification. HighlightsO_LIBasement membrane extract (BME) enlarges MSC-based Cart-Org. C_LIO_LIBME activates the SMAD pathway and inhibits the NK-kB pathway of the Cart-Org. C_LIO_LIBME promotes cartilaginous maturation and further ossification of Cart-Org. C_LI

cell biology↗

bioRxiv2023

Early acquisition of S-specific Tfh clonotypes after SARS-CoV-2 vaccination is associated with the longevity of anti-S antibodies

SARS-CoV-2 vaccines have been used worldwide to combat COVID-19 pandemic. To elucidate the factors that determine the longevity of spike (S)-specific antibodies, we traced the characteristics of S-specific T cell clonotypes together with their epitopes and anti-S antibody titers before and after BNT162b2 vaccination over time. T cell receptor (TCR) {beta} sequences and mRNA expression of the S-responded T cells were investigated using single-cell TCR- and RNA-sequencing. Highly expanded 199 TCR clonotypes upon stimulation with S peptide pools were reconstituted into a reporter T cell line for the determination of epitopes and restricting HLAs. Among them, we could determine 78 S epitopes, most of which were conserved in variants of concern (VOCs). After the 2nd vaccination, T cell clonotypes highly responsive to recall S stimulation were polarized to follicular helper T (Tfh)-like cells in donors exhibiting sustained anti-S antibody titers (designated as "sustainers"), but not in "decliners". Even before vaccination, S-reactive CD4+ T cell clonotypes did exist, most of which cross-reacted with environmental or symbiotic bacteria. However, these clonotypes contracted after vaccination. Conversely, S-reactive clonotypes dominated after vaccination were undetectable in pre-vaccinated T cell pool, suggesting that highly-responding S-reactive T cells were established by vaccination from rare clonotypes. These results suggest that de novo acquisition of memory Tfh-like cells upon vaccination may contribute to the longevity of anti-S antibody titers.

immunology↗

bioRxiv2023

CD4+ T-cell immunity of SARS-CoV-2 patients determine pneumonia development

Most humans infected with SARS-CoV-2 will recover without developing pneumonia. A few SARS-CoV-2 infected patients, however, develop pneumonia, and occasionally develop cytokine storms. In such cases, it is assumed that there is an inadequate immune response to eliminate viral infected cells and an excessive inappropriate immune response causing organ damage, but little is known about this mechanism. In this study, we used single cell RNA sequencing and mass cytometry to analyze peripheral blood T cells from patients hospitalized with proven COVID-19 infection in order to clarify the differences in host immune status among COVID-19 pneumonia cases, non-pneumonia cases, and healthy controls. The results showed that a specific CD4+ T cell cluster with chemokine receptor expression patterns, CXCR3+CCR4-CCR6+ (Th1/17), was less abundant in COVID-19 pneumonia patients. Interestingly, these CD4+ T-cell clusters were identical to those we have reported to correlate with antitumor immunity and predict programmed cell death (PD)-1 blockade treatment response in lung cancer. The Th1/17 cell percentages had biomarker performance in diagnosing pneumonia cases. In addition, CTLA-4 expression of type17 helper T cells (Th17) and regulatory T cells (Treg) was found to be significantly lower. This indicates that functional suppression of Th17 was less effective and Treg function was impaired in pneumonia cases. These results suggest that imbalance of CD4+ T-cell immunity generates excessive immunity that does not lead to viral eradication. This might be a potential therapeutic target mechanism to prevent severe viral infections. ImportanceIn this observational study, 49 consecutive patients with SARS-CoV-2 infection confirmed by PCR testing and admitted to Saitama Medical University Hospital and Saitama Medical University International Medical Centre between December 4, 2020 and January 17, 2022 were included. Of these 49 patients, 29 were diagnosed with COVID-19 pneumonia by computed tomography (CT) scan (Table 1). The unique CD4+ T-cell immunity with less abundant Th1/17 CD4+ T-cell cluster and low expression of CTLA-4 in Th17 and Treg was consistently found in SARS-CoV-2 pneumonia patients on admission and 1-week of admission. The imbalance of CD4+ T-cell immunity may contribute to develop pneumonia in SARS-CoV-2 virus infected patients by delaying viral clearance and resulting in an excessive immune response. O_TBL View this table: org.highwire.dtl.DTLVardef@1aac015org.highwire.dtl.DTLVardef@128c14dorg.highwire.dtl.DTLVardef@aacabaorg.highwire.dtl.DTLVardef@e39c8eorg.highwire.dtl.DTLVardef@13b439a_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 1C_FLOATNO O_TABLECAPTIONPatient demographics C_TABLECAPTION C_TBL

immunology↗

bioRxiv2022

Human Dectin-1 is O-glycosylated and serves as a ligand for C-type lectin receptor CLEC-2

C-type lectin receptors (CLRs) elicit immune responses upon recognition of glycoconjugates present on pathogens and self-components. While Dectin-1 is the best-characterized CLR recognizing {beta}-glucan on pathogens, the endogenous targets of Dectin-1 are not fully understood. Herein, we report that human Dectin-1 is a ligand for CLEC-2, another CLR expressed on platelets. Biochemical analyses revealed that Dectin-1 is a mucin-like protein as its stalk region is highly O-glycosylated. A sialylated core 1 glycan attached to the EDxxT motif of human Dectin-1, which is absent in mouse Dectin-1, provides a ligand moiety for CLEC-2. Strikingly, the expression of human Dectin-1 in mice rescued the lethality and lymphatic defect resulting from a deficiency of Podoplanin, a known CLEC-2 ligand. This finding is the first example of an innate immune receptor also functioning as a physiological ligand to regulate ontogeny upon glycosylation.

immunology↗

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

InterClone: Store, Search and Cluster Adaptive Immune Receptor Repertoires

B and T cell receptor repertoire data has the potential to fundamentally change the way we diagnose and treat a wide range of diseases. However, there are few resources for storing or analyzing repertoire data. InterClone provides tools for storing, searching, and clustering repertoire datasets. Efficiency is achieved by encoding the complementarity-determining regions of sequences as mmseqs2 databases. Single chain search or cluster results can be merged into paired (alpha-beta or heavy-light) results for analysis of single-cell sequencing data. We illustrate the use of InterClone with two recently reported examples: 1) searching for SARS-CoV-2 infection-enhancing antibodies in bulk COVID-19 and healthy donor repertoires; 2) identification of SARS-CoV-2 specific TCRs by clustering paired and bulk sequences from COVID-19, BNT162b2 vaccinated and healthy unvaccinated donors. The core functions of InterClone have been implemented as a web server and integrated database (https://sysimm.org/interclone). All source code is available upon request.

bioinformatics↗

bioRxiv2022

Role of the drug efflux pump in the intrinsic cefiderocol resistance of Pseudomonas aeruginosa

Cefiderocol is a novel siderophore cephalosporin antibiotic exhibiting activities against carbapenem-resistant Gram-negative bacteria including Pseudomonas aeruginosa and Enterobacteriaceae. Drug efflux pumps are reportedly involved in both intrinsic and acquired drug resistance, although their role in bacterial cefiderocol susceptibility remains poorly understood. In this study, we investigated how drug efflux pumps contribute to bacterial cefiderocol susceptibility using the efflux pump(s)-deficient and overexpressing strains of P. aeruginosa, Escherichia coli, and Salmonella enterica. We observed that the mexAB-oprM-deficient P. aeruginosa mutant displayed increased cefiderocol susceptibility compared to the wild-type strain. The overexpression of mexAB-oprM or mexXY-oprM in the mexAB-oprM-deficient mutant increased the MIC value of cefiderocol. Furthermore, the pump inhibitor phenylalanine-arginine {beta}-naphthylamide increased cefiderocol susceptibility in wild-type P. aeruginosa whereas it did not affect the susceptibility of the mexAB-oprM-deficient mutant. These data indicate that the MexAB-OprM drug efflux system contributes to the intrinsic cefiderocol resistance of P. aeruginosa. In addition, MexXY-OprM partially complemented the function of MexAB-OprM in the cefiderocol susceptibility, when expressed.

microbiology↗

bioRxiv2022

Self-organization, quality control, and preclinical studies of human iPSC-derived retinal sheets for tissue-transplantation therapy

Three-dimensional retinal organoids (3D-retinas) are a promising graft source for transplantation therapy. We previously developed self-organizing culture for 3D-retina generation from human pluripotent stem cells (hPSCs). Here we present a quality control method and preclinical studies for tissue-sheet transplantation. Self-organizing hPSCs differentiated into both retinal and off-target tissues. Gene expression analyses identified the major off-target tissues as eye-related, cortex-like, and spinal cord-like tissues. For quality control, we developed a qPCR-based test in which each hPSC-derived neuroepithelium was dissected into two tissue-sheets: inner-central sheet for transplantation and outer-peripheral sheet for qPCR to ensure retinal tissue selection. During qPCR, tissue-sheets were stored for 3-4 days using a newly developed preservation method. In a rat tumorigenicity study, no transplant-related adverse events were observed. In retinal degeneration model rats, retinal transplants differentiated into mature photoreceptors and exhibited light responses in electrophysiology assays. These results demonstrate our rationale toward self-organizing retinal sheet transplantation therapy.

neuroscience↗

bioRxiv2021

Identification, crystallization and epitope determination of public TCR shared and expanded in COVID-19 patients

T cells play pivotal roles in protective immunity against SARS-CoV-2 infection. Follicular helper T (Tfh) cells mediate the production of antigen-specific antibodies; however, T cell receptor (TCR) clonotypes used by SARS-CoV-2-specific Tfh cells have not been well characterized. Here, we first identified and crystallized public TCR of Tfh clonotypes that are shared and expanded in unhospitalized COVID-19-recovered patients. These clonotypes preferentially recognized SARS-CoV-2 spike (S) protein epitopes which are conserved among emerging SARS-CoV-2 variants. These clonotypes did not react with S proteins derived from common cold human coronaviruses, but cross-reacted with symbiotic bacteria, which might confer the publicity. Among SARS-CoV-2 S epitopes, S864-882, presented by frequent HLA-DR alleles, could activate multiple public Tfh clonotypes in COVID-19-recovered patients. Furthermore, S864-882-loaded HLA tetramer preferentially bound to CD4+ T cells expressing CXCR5. In this study, we identified and crystallized public TCR for SARS-CoV-2 that may contribute to the prevention of COVID-19 aggravation.

immunology↗

bioRxiv2021

Sequence features around cleavage sites are highly conserved among different species and a critical determinant for RNA cleavage position across eukaryotes

RNA degradation is critical for control of gene expression, and endonucleolytic cleavage- dependent RNA degradation is conserved among eukaryotes. Some cleavage sites are secondarily capped in the cytoplasm and identified using the CAGE method. Although uncapped cleavage sites are widespread in eukaryotes, comparatively little information has been obtained about these sites using CAGE-based degradome analysis. Previously, we developed the truncated RNA-end sequencing (TREseq) method in plant species and used it to acquire comprehensive information about uncapped cleavage sites; we observed G-rich sequences near cleavage sites. However, it remains unclear whether this finding is general to other eukaryotes. In this study, we conducted TREseq analyses in fruit flies (Drosophila melanogaster) and budding yeast (Saccharomyces cerevisiae). The results revealed specific sequence features related to RNA cleavage in D. melanogaster and S. cerevisiae that were similar to sequence patterns in Arabidopsis thaliana. Although previous studies suggest that ribosome movements are important for determining cleavage position, feature selection using a random forest classifier showed that sequences around cleavage sites were major determinant for cleaved or uncleaved sites. Together, our results suggest that sequence features around cleavage sites are critical for determining cleavage position, and that sequence-specific endonucleolytic cleavage-dependent RNA degradation is highly conserved across eukaryotes.

bioinformatics↗

bioRxiv2020

Identification of a recently dominate sublineage in Salmonella 4,,12:i:- sequence type 34 isolated from food animals in Japan

Salmonella Typhimurium and its monophasic variant (Salmonella 4,[5],12:i:-) are classified into nine clades. Clade 9 is composed of ST34 strains, including the Salmonella 4,[5],12:i:-European clone, which has rapidly disseminated in humans and animals worldwide since the 2000s. To reveal the microevolution of ST34/clade 9, we analyzed the whole-genome-based phylogenetic relationships of 230 Salmonella Typhimurium and Salmonella 4,[5],12:i:-strains isolated between 1998 and 2017 in Japan and other countries. We identified clade 9-2, a novel sublineage derived from the conventional Salmonella 4,[5],12:i:-clade 9 that exclusively consists of Japanese isolates. Clade 9-2 was generated by mobile genetic element-mediated stepwise genome reductions caused by IS26 and prophages. Furthermore, the recently identified strains developed further resistance to antimicrobials via the acquisition of resistance genes. During this microevolution, Salmonella 4,[5],12:i:-clade 9-2 has dominated among recent isolates from food animals in Japan via the emergence of clonally expanding and/or multiple host-adapted subclades.

microbiology↗

bioRxiv2020

Patterns of functional and structural brain information are preserved over generations

There is clear evidence of intergenerational transmission of life values, cognitive traits, psychiatric disorders, and even aspects of daily decision making. To investigate biological substrates of this phenomenon, brain has received increasing attention as a measurable biomarker and potential target for intervention. However, no previous study has quantitatively and comprehensively investigated the effects of intergenerational transmission on functional and structural brain networks from parents to their children. Here, by employing an unusually large cohort dataset, we show that patterns of functional and structural brain networks are preserved over a generation. We also demonstrate that several demographic and behavioural phenotypes have effects on brain similarity. Collectively, our results provide a comprehensive picture of neurobiological substrates of parent-child similarity, and demonstrate the usability of our dataset for investigating the neurobiological substrates of intergenerational transmission.

neuroscience↗

bioRxiv2019

Functional connectome linking child-parent relationships with psychological problems in adolescence

Paternal- and maternal-child relationships are associated with partly distinct psychobehavioral problems, which often manifest differently between boys and girls. In order to understand neural mechanisms underlying complicated mappings between child-parent relationship and adolescents problems, we used a dataset of early adolescents (N=93) and separately estimated the effects of paternal- and maternal-child relationships on resting-state functional connectivity and problems in boys and girls. General linear models identified the effects of paternal- and maternal-child relationships in different sets of functional connectivity, which we termed functional brain connectomes associated with paternal- and maternal-child relationship (FBCp and FBCm), respectively. Subsequent connectome-based models using these FBCs significantly predicted aggressive behaviors only for boys and internalizing problems selectively only girls. Lastly, a causal discovery method identified causal paths from daughter-mother relationship to FBCm, and then to daughters internalizing problems. These observations highlight sex-dependent mechanisms linking child-parent relationship, brain, and psychobehavioral problems in early adolescence.

neuroscience↗

bioRxiv2019

Salmonella genomic island 3 is an integrative and conjugative element and contributes to copper and arsenic resistance of Salmonella enterica

Salmonella genomic island 3 (SGI3) was first described as a chromosomal island in Salmonella 4,[5],12:i:-, a monophasic variant of Salmonella enterica subsp. enterica serovar Typhimurium. The SGI3 DNA sequence detected from Salmonella 4,[5],12:i:-isolated in Japan was identical to that of a previously reported one across entire length of 81 kb. SGI3 consists of 86 open reading frames, including a copper homeostasis and silver resistance island (CHASRI) and an arsenic resistance operon in addition to genes related to conjugative transfer and DNA replication or partitioning, suggesting that the island is a mobile genetic element. We successfully selected transconjugants that acquired SGI3 after filter mating experiments using the S. enterica serovars Typhimurium, Heidelberg, Hadar, Newport, Cerro, and Thompson as recipients. Southern blot analysis using I-CeuI-digested genomic DNA demonstrated that SGI3 was integrated into a chromosomal fragment of the transconjugants. PCR and sequencing analysis demonstrated that SGI3 was inserted into the 3' end of the tRNA genes pheV or pheR. The length of the target site was 52 or 55 bp, and a 55-bp attI sequence indicating generation of the circular form of SGI3 was also detected. The transconjugants had a higher MIC against CuSO4 compared with the recipient strains under anaerobic conditions. Resistance was defined by the cus gene cluster in the CHASRI. The transconjugants also had distinctly higher MICs against Na2HAsO4 compared with recipient strains under aerobic conditions. These findings clearly demonstrate that SGI3 is an integrative and conjugative element and contributes to the copper and arsenic resistance of S. enterica.

microbiology↗

bioRxiv2018

Development of the Brief Personal Values Inventory for sense of values in the Japanese general population

The Portrait Values Questionnaire (PVQ) is a widely used questionnaire for assessing sense of values; however, it has limitations, especially for children. Therefore, the present study aims to develop a questionnaire for sense of values, called the Brief Personal Values Inventory (BPVI), consisting of simple questions and a smaller number of items compared to the PVQ. We first created 12 items for the BPVI and then tested their validity and reliability in 167 Japanese general population (81 males, mean age (SD) [range]: 23.4 (8.2) [15-57] years). Each of these items was correlated with one or more values in the PVQ-57. The BPVI items covered all higher-order values in Schwartzs theory (Openness to Change, Self-Enhancement, Conservation, and Self-Transcendence). In sum, the BPVI has an acceptable criterion-related validity and corresponds to higher-order values in Schwartzs value theory. The BPVI is suitable for a reliable and direct comparison of sense of values between children and adults, which may be useful for elucidating the developmental pathway of personal sense of values.

scientific communication and education↗