Biology subjects

Sakaguchi, S.

Publications and source records attributed to Sakaguchi, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Antiviral activity of anisomycin against chikungunya virus

Chikungunya virus (CHIKV) is a globally prevalent arbovirus transmitted by Aedes mosquitoes, which causes acute fever accompanied by debilitating joint pain that can persist for extended periods. Despite the significant public health impact and an increasing incidence worldwide, antiviral treatment targeting CHIKV has not been clinically approved. In this study, we screened compounds using a newly developed In-Cell ELISA-based assay and CHIKV Indian Ocean Lineage (IOL) and found that an antibiotic derived from Streptomyces bacteria, anisomycin, potentially inhibited CHIKV. The selectivity index of anisomycin was favorable for anti-CHIKV activity, with 50% effective concentration (EC50) of 200 pM and 50% cytotoxic concentration (CC50) of 390 nM in Vero cells. This robust inhibitory activity against CHIKV was confirmed in a human cell line and against a CHIKV East/Central/South African (ECSA) lineage. These effects of anisomycin were apparently independent of its functions as a translation inhibitor and mitogen-activated protein kinase (MAPK) pathway stimulator. These findings, together with the finding that anisomycin suppressed the production of infectious CHIKV virions, suggested that anisomycin inhibits CHIKV via a distinct mechanism. Further mechanistic insights were gained through genetic analyses of anisomycin-resistant mutants, which revealed that a single amino acid substitution (G117R) in the macrodomain of CHIKV nsP3 confers resistance to anisomycin. Importantly, anisomycin reduced footpad swelling and viremia in mice during the early days of CHIKV infection, indicating its therapeutic potential. Given its inhibitory activity against other arboviruses, our study positions anisomycin as a promising lead inhibitor for the future development of broad-spectrum antiviral drugs, including CHIKV. Author summaryChikungunya fever (CHIKF) is a mosquito-borne disease caused by the chikungunya virus (CHIKV) and is characterized by fever, rash, and arthralgia. Although most persons infected with CHIKV recover within days, joint pain and severe complications can persist. However, the management of CHIKF is limited to symptom relief, and specific antiviral treatments are not available. Our study focused on identifying potential inhibitors of CHIKV infection. We found that the natural alkaloid, anisomycin, inhibited CHIKV replication in cultured cells in vitro using a novel screening assay and a chemical compound library. Interestingly, the mechanism by which anisomycin blocks CHIKV infection likely differs from its currently known effects, suggesting a distinct mode of inhibition. We also identified an amino acid change in a nonstructural protein that conferred resistance to anisomycin, providing insights into a viral target of anisomycin. Importantly, anisomycin reduced disease symptoms and viremia in mouse models of CHIKV in vivo. Because anisomycin inhibits other mosquito-borne viruses, our findings suggest that it could serve as a basis for developing broad-acting antiviral drugs.

microbiology↗

bioRxiv2026

Monju: Multi-criteria clustering in single-cell omics

Clustering is a fundamental step in single-cell omics analysis. Although single-cell omics data can, in principle, be partitioned according to multiple biologically meaningful criteria, existing methods typically cluster cells using a single criterion. To address this problem, we developed Monju, a multi-criteria clustering method based on a deep generative mixture model. Monju divides cells into biologically reasonable submodels, each of which is equipped with an interpretable latent space. Furthermore, although the partitioning of cells into submodels varies across random seeds, each solution remains biologically plausible, collectively yielding multi-criteria clustering. Moreover, by integrating these multiple clustering solutions to perform meta-clustering, Monju enables the assessment of cluster stability. We applied Monju to human peripheral blood CITE-seq data and demonstrated that it can achieve multi-criteria clustering. Monju therefore provides a powerful and practical framework for dissecting cellular heterogeneity from multiple biological perspectives.

bioinformatics↗

bioRxiv2026

Massively multiplex multimodal chemical screens at single-cell resolution

Recent applications of scRNA-seq for massively multiplexed chemical screens have enabled comprehensive profiling of drug responses at unprecedented scale and resolution. However, current assays remain limited to RNA readouts, lacking information on other phenotypic and mechanistic layers such as chromatin accessibility, protein abundance and post-translational modifications. Here, we introduce a scalable framework for multimodal chemical screens, combining parallel small-molecule perturbations with multimodal readouts. We extend existing experimental platforms into icCITE-plex and DOGMA-plex, enabling joint profiling of RNA, protein, and epigenomic responses to thousands of chemical perturbations in parallel. To systematically decode the regulatory circuitry underlying these responses, we develop MoCAVI, a contrastive analysis framework that disentangles the effect of small molecules from control variation in multimodal measurements, and PERCISTRA, a pipeline that infers causal links between chromatin accessibility and gene expression. Applied across ~410,000 primary T cells under ~2,800 conditions, our approach resolves compound-specific mechanisms, highlights off-target effects, and links chromatin accessibility changes to transcription factor networks in primary T cells. Our results establish a generalizable platform for profiling and analyzing cellular responses to chemical perturbations across multiple modalities.

genomics↗

bioRxiv2026

RdRpCATCH: A unified resource for RNA virus discovery using viral RNA-dependent RNA polymerase profile Hidden Markov models

Recent advances in large-scale sequence mining have expanded our knowledge of RNA virus diversity. Most genome mining approaches for detecting RNA viruses that encode RNA-dependent RNA polymerase (RdRp) rely on identifying this conserved protein by employing profile Hidden Markov Models (pHMMs) to scan sequencing datasets. Recently, several new pHMM databases for RdRp detection have been released, each following distinct design principles. However, their relative performance is unclear and their accessibility to users without specialized computational expertise is limited. Here, we introduce the RdRp Collaborative Analysis Tool with Collections of pHMMs (RdRpCATCH: https://github.com/dimitris-karapliafis/RdRpCATCH), developed to consolidate publicly available RdRp pHMM resources into a single, accessible platform. RdRpCATCH enables the scanning of (meta)transcriptomic assemblies to discover RNA viruses and provides subsequent taxonomic annotation of detected contigs. A comparative analysis of RdRp pHMM databases reveals that most are highly effective at detecting known diversity of RNA viruses while minimizing false positives, supporting their joint use within RdRpCATCH. RdRpCATCH is distributed as both a conda package and a web server application (https://rdrpcatch.bioinformatics.nl), facilitating access for researchers with diverse expertise. By integrating multiple pHMM resources, this unified framework addresses fragmentation in the field and reduces technical barriers, enabling comprehensive viral discovery.

bioinformatics↗

bioRxiv2026

Cell-intrinsic compliance mechanism enables release of tensile stress to prevent tissue rupture

Contractile forces are necessary to sculpt tissue structures and organ shapes during morphogenesis. In the early embryo, this presents an engineering challenge as the deforming tissue can be relatively large, while the forces thus generated might be poorly compartmentalized, generating tensile stresses that can cause damage if unmitigated. Here we show that during Drosophila gastrulation, the squamous morphogenesis of the extraembryonic amnioserosa functions mechanically to release tensile stresses yielded from the neighboring ectodermal convergent-extension and mesodermal invagination. Amnioserosa master regulator Zen transcriptionally silences shroom to endow it with low junctional actomyosin stresses, thereby ensuring high mechanical compliance. Loss of Zen, or targeted ectopic expression of Shroom in the amnioserosa using a novel optogenetic Gal4 system, leads to increased junctional myosin, thereby causing load-dependent tissue ruptures. Our data establish a previously unknown function for the Drosophila extraembryonic tissue, whereby cell-intrinsic mechanical compliance prevents tissue rupture to mitigate inter-tissue mechanical conflicts.

developmental biology↗

bioRxiv2025

Bypassing the Batch Effects to Improve the Reusability of RAD-seq Data: A Case Study of Recurrent Hybridization in the Japanese Torreya Species Complex

Understanding the evolutionary effects of natural hybridization in gymnosperms remains limited due to their large genome sizes and frequent reliance on sparce molecular data. In this study, we reassessed the evolutionary history and taxonomy of the Japanese Torreya species complex (T. nucifera) by integrating the morphological characteristics, environmental niches, and molecular evidence. We developed RADADOR version 2 to overcome allele dropout (ADO) issues in RAD-seq data sets. This version of RADADOR enabled us to recover ADO loci using low-coverage whole genome sequencing (lc-WGS) data ([~]5-10X coverage). We integrated previously generated plastome and RAD-seq data with whole genome data to build robust, genome-wide phylogenies. Subsequently, we employed PhyloNet to detect hybridization events in Torreya and utilized a fossilized birth-death model to estimate the formation times of Japanese Torreya species. Our phylogenetic results indicated conflicting nuclear and plastome topologies and suggested two historical hybridization events in Japanese Torreya. One ancient hybridization between T. nucifera and a North American lineage likely contributed to the origin of T. fruticosa, while a more recent event may have generated a putative hybrid in regions where their distributions overlap. Integrating the lc-WGS data and RAD-seq data in a reproducible framework revealed the complex reticulate evolution of Torreya in Japan and underscores the repeated contribution of inter-specific hybridization to the evolution of gymnosperms.

evolutionary biology↗

bioRxiv2025

Generation of antigen-specific and functionally stable Treg cells from effector/memory T cells for cell therapy of immunological diseases

One strategy for antigen-specific immunosuppression is to convert antigen-specific conventional T cells (Tconvs) into Foxp3+ regulatory T cells (Tregs) that are as stably suppressive as naturally occurring Tregs (nTregs). To achieve the conversion in vitro for mice and humans, we induced high Foxp3 expression in antigen- and IL-2-stimulated Tconvs by CDK8/19 inhibition, and established Treg-specific epigenetic changes by depriving CD28 co-stimulation during in vitro Treg induction to specifically promote the expression of Treg signature genes, especially Foxp3. Repeating this process, with intermittent resting cultures containing IL-2 only, enabled in a short duration efficient conversion of naive as well as effector/memory CD4+ Tconvs, including Th1, Th2 and Th17 cells, into Foxp3+ Tregs, which were similar to nTregs in transcription and epigenetic modification. Induced Tregs (iTregs) thus generated were indeed functionally and phenotypically stable in vivo and effectively suppressed inflammatory bowel disease and graft-versus-host disease in mouse models. Adoptive cell therapy with such effector/memory Tconv-derived, functionally stable, iTregs would be able to achieve antigen- and disease-specific treatment of immunological diseases. One Sentence SummaryAntigen-specific and functionally stable Treg cells can be generated in vitro from effector/memory T cells for cell therapy of immunological diseases.

immunology↗

bioRxiv2025

Disentanglement of batch effects and biological signals across conditions in the single-cell transcriptome

Batch effects, which arise due to technical variations across different experimental factors, pose a significant challenge for single-cell transcriptomic analysis. Although various batch correction methods have been developed to mitigate these effects, they often indiscriminately mix data from different batches, leading to the removal of biologically meaningful signals. This limitation hinders comparative analyses across multiple conditions, an essential aspect of scientific research. Recent approaches attempt to address this issue by mapping data to separate spaces, but they prevent direct comparisons between conditions. Here, we propose Kanade, a batch correction method based on a variational autoencoder. Kanade explicitly disentangles batch effects from biological signals by specializing latent variables for different types of information. Using both simulated and real datasets, we demonstrate that Kanade selectively correct batch effects while preserving essential biological features, enabling more accurate comparative analyses in single-cell transcriptomics.

bioinformatics↗

bioRxiv2025

Oral antigen exposure under co-stimulation blockade generates Treg cells to establish immune tolerance despite prior sensitization

Antigen-specific oral tolerance is effective in preventing harmful immune responses in antigen-non-sensitized animals but difficult to be induced in those already antigen-primed. Here, we show in mice that feeding of antigen-containing diet generates peripherally derived regulatory T (pTreg) cells that exhibit a tissue-adapted effector phenotype. The antigen feeding also enables the generated pTreg cells to acquire Treg-specific epigenomic changes in Treg signature genes including Foxp3, hence the stability of Treg-specific function. Cessation of antigen feeding, however, results in decline in oral tolerance with diminution of pTreg cells. Transcriptomic analysis has revealed that the induced pTreg cells predominantly express CD101. CD101+ Treg cells with a similar phenotype and epigenetic alterations can also be generated in vitro from antigen-primed naive CD4+ T cells by blockade of CD28-mediated co-stimulation during TGF-{beta}-dependent Treg induction. Furthermore, in vivo CD28 signal blockade by CTLA-4-immunoglobulin fusion protein (CTLA4-Ig) before antigen feeding can establish oral tolerance in the mice precedingly antigen-sensitized by a non-oral route. The blockade facilitates differentiation of antigen-specific conventional T cells into CD101+ pTreg cells. Thus, continuous oral antigen administration combined with CD28 co-stimulation blockade generates CD101+ antigen-specific functionally stable pTreg cells, which can establish long-term systemic antigen-specific immune tolerance even in antigen-pre-sensitized animals.

immunology↗

bioRxiv2025

Joint single-cell measurements of surface proteins, intracellular proteins and gene expression with icCITE-seq

The development of single-cell RNA-sequencing assays has transformed our understanding of cellular and tissue heterogeneity, yielding significant insights into disease biology and its underlying mechanisms. In this work, we describe icCITE-seq (intracellular cellular indexing of transcriptomes and epitopes), a scalable method that simultaneously measures surface and intracellular protein levels alongside gene expression across thousands of cells. We validate the specificity of intracellular staining and demonstrate the utility of this multi-omic approach in interrogating phenotypic cellular states through targeted genetic perturbations in primary human T cells. icCITE-seq enables systematic profiling of gene expression, coupled with cytoplasmic, nuclear and PTM epitopes, providing an integrated approach towards understanding cellular identity, complexity and disease regulatory mechanisms.

immunology↗

bioRxiv2024

Loss of PI3Kδ activity drives autoimmune colitis by impairing extrathymic Treg differentiation

Peripherally-derived regulatory T cells (pTregs) have a prominent role in maintaining intestinal immune homeostasis. In cases of phosphoinositide-3-kinase {delta} (PI3K{delta}) inactivation, such as in patients receiving PI3K{delta} inhibitor idelalisib as a cancer treatment, breakdown of intestinal immune tolerance occurs frequently in the form of diarrhoea and colon inflammation. In a mouse model of systemic PI3K{delta} inactivation, both enhancement of anti-tumor immunity and colitis have been described, as a result of Treg impairment. However, in view of the critical role for Tregs in the prevention of systemic autoimmunity, the basis for such tissue-restricted breach of immune tolerance upon loss of PI3K{delta} function is not yet understood. We report here that mice lacking PI3K{delta} activity do not suffer a general defect in Treg immunosuppression, but specifically fail to develop Helios- pTregs in the colon. We demonstrate reduced extrathymic Treg induction, in vitro and in vivo, from naive CD4+ T cells with inactive PI3K{delta}, along with dysregulation of a tissue-resident phenotype. These results suggest a non-redundant role for PI3K{delta}-dependent pTreg differentiation in maintaining tolerance to commensal microbial antigens in the gut.

immunology↗

bioRxiv2024

Th17 cells with a pathogenic signature in joints of ZAP-70 mutant arthritic mice harbor unique TCR repertoires that share features with WT Tregs

Mutations in the ZAP-70 gene that cause moderate attenuation of T cell receptor (TCR) signaling in mice can result in autoimmune manifestations. One explanation for this pathology is a shift in the regulatory-conventional (Treg-Tconv) T cell repertoire composition. To test this hypothesis, we characterized the single-cell gene expression profiles and TCR repertoires of Tconv and Treg CD4+ T cells of arthritic (ZAC), poised (SKG) ZAP-70 mutant, and wild-type (WT) mice. We identified a group of Th17 cells which exhibited a pathogenic signature and occurred exclusively in inflamed joints of ZAC mice. Such pathogenic signature was uniquely detected in CD4+ T cells obtained from inflamed joints of RA patients. Overall, the Tconv repertoires of ZAP-70 mutant mice were increasingly similar to the repertoires of WT Tregs, and this effect was most notable in the subset of pathogenic Th17 cells. Our results support a model where, upon moderate ZAP-70-mediated signal weakening, T cells that would normally develop into Tregs, instead develop into self-reactive Tconvs, resulting in a breakdown in self-tolerance and susceptibility to autoimmune arthritis.

immunology↗

bioRxiv2024

HDAC1 controls the generation and maintenance of effector-like CD8+ T cells during chronic viral infection

CD8+ T cell exhaustion is a complex process that involves the differentiation of persistently activated CD8+ T cells into functionally distinct cell subsets. Here, we investigated the role of the key epigenetic regulator histone deacetylase 1 (HDAC1) in the differentiation of exhausted T (Tex) cells during chronic viral infection. We uncovered that HDAC1 controls the generation and maintenance of effector-like CX3CR1+ Tex cells in a CD8+ T cell-intrinsic manner. Deletion of HDAC1 led to expansion of an alternative Tex cell subset characterized by high expression of T cell exhaustion markers, and this was accompanied by elevated viremia. HDAC1 knockout altered the chromatin landscape in progenitor Tex cells, abrogated the expression of effector-like signature genes and interfered with cell fate specification toward the CX3CR1+ Tex cell subset. We conclude that HDAC1 is functionally required for controlling viral load during chronic infection by ensuring adequate CX3CR1+ Tex cell subset differentiation. HighlightsO_LIHDAC1 promotes the generation of CX3CR1+ effector-like Tex cell subsets in chronic viral infection in a CD8+ T cell-intrinsic manner. C_LIO_LIDeletion of HDAC1 leads to an increase of a cell subset enriched in exhaustion markers and is accompanied with elevated viremia. C_LIO_LIHDAC1 is required for the maintenance of the CX3CR1+ Tex cell pool. C_LIO_LIHDAC1 deletion alters the chromatin landscape at effector-like signature gene loci in progenitor Tex cells. C_LI

immunology↗

bioRxiv2023

Thymically imprinted differential responsivity of naive CD4 T cells to IL2 results in a heterogeneity of both Treg induction and subsequent effector functioning

Thymic selection predisposes naive T cells to particular outcomes when challenged later with cognate antigen, whether the antigen is self or foreign. This suggests that there is an inherent heterogeneity of functioning among T cells within the naive population (both CD4 and CD8s), and that each T cell, as part of its thymic development, is given a certain programming which will affect its eventual fate decisions. In this project, we looked at the primary effects of this thymic imprinting on the conversion of naive CD4 T cells into Tregs. Further, using an induced-Treg-reporter system, we exam the impact of thymic imprinted heterogeneity on effector functionality and identity stability. We report that naive T cell differential responsivity to cytokines leads to the observed difference in Treg induction, and that the Tregs induced from T cells of different self-affinities maintain a heterogeneity of effector function and identity.

immunology↗

bioRxiv2023

Ikzf1 association with Foxp3 for Foxp3-dependent gene repression in Treg cells: induction of autoimmunity and tumor immunity by disrupting the association

The transcription factor Foxp3 specifically expressed in regulatory T (Treg) cells controls Treg function by repressing some genes and activating others. We have shown here that the transcription factor Ikzf1 associates with Foxp3 via its exon 5 (called IkE5) and that conditional deletion of IkE5 up-regulated the genes, including Ifng, normally repressed by Foxp3 upon TCR stimulation. IkE5-deletion in Treg cells indeed incurred IFN-{gamma} overproduction, which destabilized Foxp3 expression and impaired suppressive function, consequently producing fatal systemic autoimmune diseases and evoking strong anti-tumor immunity. In addition, pomalidomide, which degrades IKZF1 and IKZF3, induced IFN-{gamma} overproduction in human Treg cells. Mechanistically, the Foxp3/Ikzf1/Ikzf3 complex exerted gene-repressing function by competing with epigenetic co-activators, such as p300 and NFAT1, for binding to the target gene loci via chromatin remodeling. Collectively, the association of Ikzf1 with Foxp3 is essential for repressive function of Foxp3, and can be targeted to control autoimmunity and tumor immunity.

immunology↗

bioRxiv2023

Soluble CTLA-4 mainly produced by Treg cells inhibits and resolves type 1 inflammation but allows type 2 immunity

CTLA-4 exists as membrane (mCTLA-4) and soluble (sCTLA-4) forms. Here, we show that effector-type regulatory T cells (Tregs) are main sCTLA-4 producers in basal and inflammatory states with distinct kinetics upon TCR stimulation. Mice specifically deficient in sCTLA-4 production exhibited spontaneous activation of Th1, Th17, Tfh, and Tc1 cells, autoantibody and IgE production, M1-like macrophage polarization, and impaired wound healing. In contrast, sCTLA-4-intact mCTLA-4-deficient mice, when compared with double-deficient mice, developed milder systemic inflammation and showed predominant activation/differentiation of Th2, M2-like macrophages, and eosinophils. Consistently, recombinant sCTLA-4 inhibited in vitro differentiation of naive T cells towards Th1 through CD80/CD86 blockade on antigen-presenting cells, but did not affect Th2 differentiation. Moreover, sCTLA-4-intact mCTLA-4-deficient Tregs effectively suppressed Th1-mediated experimental colitis whereas double-deficient Tregs did not. Thus, sCTLA-4 production by Tregs during chronic inflammation is instrumental in controlling type 1 immunity while allowing type 2 immunity to dominate and facilitate inflammation resolution.

immunology↗

bioRxiv2023

Single-cell transcriptome landscape of circulating CD4+ T cell populations in human autoimmune diseases

CD4+ T cells are a key mediator of various autoimmune diseases; however, how they contribute to disease development remains obscure primarily because of their cellular heterogeneity. Here, we evaluated CD4+ T cell subpopulations by decomposition-based transcriptome characterization together with canonical clustering strategies. This approach identified 12 independent transcriptional gene programs governing whole CD4+ T cell heterogeneity, which can explain the ambiguity of canonical clustering. In addition, we performed a meta-analysis using public single-cell data sets of over 1.8M peripheral CD4+ T cells from 953 individuals by projecting cells onto the reference and cataloged cell frequency and qualitative alterations of the populations in 20 diseases. The analyses revealed that the 12 transcriptional programs were useful in characterizing each autoimmune disease and predicting its clinical status. Moreover, genetic variants associated with autoimmune diseases showed disease-specific enrichment within the 12 gene programs. The results collectively provide a landscape of single-cell transcriptomes of CD4+ T cell subpopulations involved in autoimmune disease.

immunology↗

bioRxiv2022

The guanine nucleotide exchange factor Rin-like acts as a gatekeeper for T follicular helper cell differentiation via regulating CD28 signaling

T follicular helper (Tfh) cells are essential for the development of germinal center B cells and high-affinity antibody producing B-cells in human and mice. Here, we identify the guanine nucleotide exchange factor (GEF) Rin-like (Rinl) as a negative regulator of Tfh generation. Loss of Rinl leads to an increase of Tfh in aging, upon in vivo immunization and acute LCMV Armstrong infection in mice, and in human CD4+ T cell in vitro cultures. Further, adoptive transfer experiments using WT and Rinl-KO naive CD4+ T cells unraveled T cell-intrinsic functions of Rinl. Mechanistically, Rinl regulates CD28 internalization and signaling, thereby shaping CD4+ T cell activation and differentiation. Thus, our results identify the GEF Rinl as a negative regulator of global Tfh differentiation in an immunological context and species-independent manner, and furthermore connect Rinl with CD28 internalization and signaling pathways in CD4+ T cells, demonstrating for the first-time the importance of endocytic processes for Tfh differentiation. HighlightsO_LIRinl-KO CD4+ T cells show increased Tfh differentiation in a context independent manner C_LIO_LIThe regulation of Tfh differentiation is T cell-intrinsic C_LIO_LIRinl controls CD28 endocytosis and shapes Tfh-specific CD28 signal transduction C_LIO_LIHuman Tfh differentiation is regulated by Rinl C_LI

immunology↗