Biology subjects

Sakai, H.

Publications and source records attributed to Sakai, H..

At least 19 recordsLinked to original sources

bioRxiv2026

Androgen receptor determines skeletal muscle sexual dimorphism

The molecular and functional bases of sexual dimorphism in skeletal muscle remain poorly understood. The androgen receptor (AR) is a major regulator of sex-biased gene expression in muscle, but its genomic targets and associated coregulators in vivo are incompletely defined. Using ChIL-seq and an AirID-AR knock-in mouse, we mapped AR-bound genes and AR-associated proteins in skeletal muscle and identified histone deacetylase-linked corepressors. We further identified myosin binding protein H (Mybph) as a female-biased AR-repressed gene conserved in mouse and human muscle. Mybph loss disrupted sarcomeric organization and selectively delayed postinjury force recovery in female mice. These findings define an in vivo AR regulatory network and identify AR-dependent Mybph repression as a potential mechanism contributing to skeletal muscle sexual dimorphism.

molecular biology↗

bioRxiv2026

Human PHOSPHO2 exhibits Mg2+-dependent phospholipid phosphatase activity

Phosphatidic acid (PA) phosphatase (PAP) is an enzyme that plays a major role in lipid signaling by controlling the cellular levels of two lipid secondary messengers: its substrate, PA, and its product, diacylglycerol. Two types of mammalian PAPs have been reported to date. Type 1 PAP (PAP1) is an Mg2+-dependent, N-ethylmaleimide (NEM)-sensitive cytosolic enzyme (EC 3.1.3.4), whereas type 2 PAP (PAP2), also known as phospholipid phosphate (PLPP) (EC 3.1.3.113), is an Mg2+-independent, NEM-insensitive transmembrane protein. PAP2 also hydrolyzes other bioactive lipids such as lyso-PA (LPA), sphingosine-1-phosphate (S1P), and ceramide-1-phosphate (C1P). Here, we purified human phosphatase orphan 2 (PHOSPHO2), a putative cytosolic phosphatase containing a haloacid dehalogenase-like domain, and characterized its enzymological properties in vitro. Purified PHOSPHO2 displays Mg2+-dependent, NEM-sensitive phosphatase activities toward PA, LPA, S1P, C1P, and glycerol-3-phosphate (G3P) in vitro. Moreover, PHOSPHO2 showed substrate selectivity for PA molecular species containing shorter saturated fatty acids such as lauric acid and myristic acid, or polyunsaturated fatty acids such as docosahexaenoic acid and arachidonic acid. The PAP activity of PHOSPHO2, but not its other phosphatase activities, was strongly enhanced in the presence of phosphatidylcholine and phosphatidylethanolamine, major components of the cell membranes. These results indicate that mammalian PHOSPHO2 is a novel cytosolic PLPP that primarily functions as a PAP on cytoplasm-facing membranes.

biochemistry↗

bioRxiv2026

Therapeutic Potential of the Novel Monoclonal Antibody 7-4G against HBsAg in a Mouse Model of Chronic Hepatitis B Virus Infection

Chronic hepatitis B virus (HBV) infection remains a major global health challenge because current antiviral therapies rarely achieve complete viral clearance. We evaluated the antiviral activity of a newly developed monoclonal antibody, 7-4G mAb, directed against the hepatitis B surface antigen (HBsAg). The antibody showed specific binding to the p27 component of HBsAg and efficiently removed HBV-related particles from patient serum in vitro. Significant HBV neutralizing activity of 7-4G mAb was observed in primary human hepatocytes and in humanized mouse models. In persistently HBV-infected PXB mice, a single administration of 7-4G mAb, either alone or in combination with another monoclonal antibody, reduced serum HBsAg levels and HBV DNA levels by two orders magnitude for two weeks after the treatment. In half of the treated mice, suppression of both viral markers was maintained through the study period, whereas rebound occurred within three to four weeks in the remaining animals. In addition, 7-4G mAb enhanced the HBV DNA-lowering effect of entecavir, a known anti-HBV drug. These findings support the further development of 7-4G mAb as part of an innovative HBV treatment strategy, addressing limitations of existing therapies and advancing toward a more effective HBV management solution.

immunology↗

bioRxiv2026

Elucidation of the anti-inflammatory mechanism of isoliquiritigenin from Glycyrrhiza uralensis using activity-based protein profiling

Glycyrrhiza uralensis is a widely used medicinal plant present in more than 70% of Kampo formulations in Japan owing to its diverse pharmacological activities, including immunomodulatory, antitumor, and antioxidant effects. Isoliquiritigenin (ILG), a major chalcone constituent of G. uralensis, exhibits anti-inflammatory activity; however, its molecular mechanism remains unclear. Here, we employed an activity-based protein profiling approach to identify the molecular targets of ILG. Given that the ,{beta}-unsaturated carbonyl moiety of ILG can covalently react with reactive cysteine residues via nucleophilic addition, we used an iodoacetamide-based probe to globally profile cysteine-reactive proteomes. The comparative analysis between ILG- and vehicle-treated RAW 264.7 macrophages identified cysteine 65 (Cys65) of lipocalin-type prostaglandin D2 synthase (L-PGDS) as a potential covalent target. ILG treatment did not alter L-PGDS expression levels, indicating that reduced probe labeling reflects direct covalent competition rather than changes in expression. Consistently, ILG significantly suppressed prostaglandin D2 (PGD2) production, comparable to the selective L-PGDS inhibitor AT-56. Although both ILG and AT-56 reduced interleukin-6 expression, ILG exerted a stronger inhibitory effect. Our results demonstrate that covalent inhibition of L-PGDS and subsequent suppression of PGD2 production represent a key mechanism underlying the anti-inflammatory activity of ILG.

biochemistry↗

bioRxiv2026

Senolytic targeting of CAF-induced KRT17+ colon cancer cells inhibits metastatic invasion

Metastasis remains the leading cause of cancer mortality, yet effective strategies to eliminate metastasis-initiating cells are lacking. Here, we dissected intratumoral heterogeneity in colon cancer using single-cell analyses and identified a KRT17+ slow-cycling cancer cell population that exhibits features of metastasis-initiating cells (L1CAM) and senescent-like cells (CDKN2A, BCL2L1). Spatial transcriptomics and immunostaining revealed that these cells localize at tumor-stroma interfaces, where they are closely associated with TGF-{beta}1-producing subset of cancer-associated fibroblasts (CAFs) and exhibit SMAD3 activation. Mechanistically, TGF-{beta}1 induces KRT17 expression in patient-derived cancer cells, while co-culture with CAFs drives the emergence of KRT17 migratory cells in a KRT17-dependent manner. Functionally, genetic ablation of KRT17 or senolytic targeting of BCL2L1 suppresses peritumoral invasion and liver metastasis in xenograft models. Clinically, KRT17 cells co-localize with TGF-{beta}1 CAFs, and their co-expression with L1CAM correlates with advanced disease stage. These findings support a model in which stromal TGF-{beta} signaling promotes the emergence of a KRT17 invasive cancer cell state with senescence-associated features and suggest that senolytic strategies may represent a potential approach to limit metastatic progression in colon cancer.

cancer biology↗

bioRxiv2026

Rice Annotation Project Database (RAP-DB): literature-curated gene annotation and integrated omics resources for rice functional genomics and molecular breeding

High-throughput sequencing technologies have enabled the generation of high-quality reference genomes for numerous rice cultivars. However, inferring gene functions, associated phenotypes, and causal variants from these sequences remains challenging. The Rice Annotation Project Database (RAP-DB; https://rapdb.dna.affrc.go.jp) is a curated genomic resource that provides comprehensive gene annotations for the reference genome of Oryza sativa ssp. japonica cv. Nipponbare. Since its major update in 2013, gene models and functional annotations have been continuously revised through expert manual curation of newly published literature related to rice genes. As of March 2025, a total of 6,631 transcripts corresponding to 6,371 loci have been curated based on 4,699 peer-reviewed publications. These curated genes are functionally characterized and are frequently associated with agronomic traits, including yield components, stress tolerance, and disease resistance. To support molecular breeding, RAP-DB now provides a curated catalogue of 904 agronomically important loci, including gene symbols, functional descriptions, and associated traits, together with more than 1,000 functionally characterized alleles compiled from the literature. In addition to in-house expert curation, RAP-DB integrates community-curated datasets for major gene families, such as WRKY transcription factors, S-domain receptor-like kinases, and leucine-rich repeat-containing receptors, thereby expanding coverage of key regulatory and defense-related genes. RAP-DB also incorporates reanalyzed RNA sequencing expression profiles alongside microarray-based expression data and co-expression networks, offering gene-centric views of expression patterns across tissues, conditions, and developmental stages. Furthermore, RAP-DB is linked to genome-wide variation datasets from diverse rice varieties through the TASUKE+ genome browser, enabling exploration of allelic diversity across varieties. To enhance annotation quality and long-term sustainability, AI-assisted literature screening and a web-based feedback system have been introduced, allowing users to submit corrections to gene models and report newly characterized genes or relevant publications. Together, these developments strengthen RAP-DB as a primary, literature-based gene annotation resource and provide a practical foundation for molecular breeding in rice.

bioinformatics↗

bioRxiv2025

Peculiar Pigment Pattern and Population Profile of a Poisonous Pufferfish

Pufferfish are well-known for their toxicity, yet they also exhibit a remarkable diversity of pigment patterns. Mushifugu (Takifugu exascurus) is a pufferfish endemic to Japans coastal waters and is characterized by conspicuous labyrinthine patterns. Despite being recorded along both the Sea of Japan and the Pacific coasts, it has a limited distribution and is infrequently observed. Aside from its unique body pattern, mushifugu shows little to no morphological differences from other Takifugu species, often leading to speculation that it may be an interspecific hybrid. In addition, previous theoretical and empirical studies have shown that complex camouflage-like labyrinthine patterns can emerge through the pattern blending caused by hybridization between spotted species, providing support for this possibility. Here, we investigate the phylogenetic origin of mushifugu and its distinctive pattern through population structure analysis and demographic inference in comparison with its closest spotted relative, komonfugu (T. flavipterus). Mitochondrial DNA (mtDNA) analysis revealed two regional haplogroups within mushifugu--one in the Sea of Japan (SJ) and the other in the Pacific Ocean (PO). In the haplotype network, the SJ haplogroup formed a distinct cluster, whereas the PO haplogroup appeared as its own cluster connected to the komonfugu haplogroup. By contrast, genome-wide SNP analyses indicated limited structure between the SJ and PO mushifugu populations, while clearly separating mushifugu from komonfugu. Coalescent-based demographic inference suggested that the two species diverged following a bottleneck event in the early Pleistocene. These results confirm that mushifugu is a distinct species rather than a recent interspecific hybrid. Nevertheless, evidence of introgression was detected in both mitochondrial and nuclear genomes, suggesting multiple episodes of past hybridization between mushifugu and komonfugu, highlighting the potentially complex evolutionary processes shaping Takifugu species and their pigment patterns.

evolutionary biology↗

bioRxiv2025

A scalable proteogenomic framework for dissecting phospho-signaling pathways in primary immune cells

Signaling networks modulated by post-translational modifications orchestrate cellular responses to external cues. Traditional approaches to study these pathways lack the throughput to systematically capture the causal architecture of these signaling pathways at scale. Here, we present an integrated proteogenomic framework that combines saturating genetic perturbations with high-throughput proteomics to systematically map cytokine-induced signaling in primary human T cells. Supporting this framework is simplePhos, a streamlined, low-input phosphoproteomics workflow that enables scalable, time-resolved analysis without the requirement for specialized equipment or robotics. We extensively validate the simplePhos pipeline by applying inflammatory stimuli, including type I and II interferons, lipopolysaccharide, and Sendai virus to primary T cells and myeloid cells, establishing foundational datasets in these treatment contexts. Ultimately, using type I interferon signaling in genetically modified T cells as a model, we demonstrate that combined application of genetic alterations and proteomic analyses can map key signaling nodes in primary immune cells. This represents a powerful strategy to mechanistically interrogate phospho-signaling networks in human immune cells, with broad applications in translational immunology and therapeutic development.

systems biology↗

bioRxiv2025

Multi-omics profiling with indoor-unmanned phenotyping reveals drought adaptation through constitutive ABF1 expression in wild rice

Improving drought resistance is crucial for stable crop production under climate change. Identifying the mechanisms of drought resistance using diverse genetic resources, including crop wild relatives, would be beneficial for molecular breeding. Here, we developed an indoor, unmanned phenotyping platform that can noninvasively and automatically collect temporal data on plant responses to drought stress. Using this system, we analyzed the phenotypic, transcriptomic, and environmental data of four cultivated rice varieties and five wild relatives. Multi-omics analysis revealed that one wild rice species exhibited drought adaptation through the constitutive expression of ABSCISIC ACID RESPONSIVE ELEMENT-BINDING FACTOR 1 (ABF1), which encodes a transcription factor that regulates drought resistance, before drought stress. Drought testing of introgression lines of cultivated rice with constitutive ABF1 expression revealed higher drought tolerance than in cultivars without a growth penalty. Our findings suggest that constitutive ABF1 expression contributes to drought adaptation in both cultivated and wild rice.

plant biology↗

bioRxiv2025

Feline leukaemia virus subgrouping using the viral interference assay

Feline leukaemia virus subgroup A (FeLV-A) is transmitted among cats, and FeLV subgroups are frequently generated de novo. We investigated the frequency of detection of subgroups using interference assays in 50 cases. FeLV-A infection alone was detected in 38% of cases, whereas co-infection with both FeLV-A and FeLV-B was observed in 62% of cases. No cases of FeLV-B infection alone were observed. Cases of co-infection with FeLV-A and FeLV-B showed a higher prevalence than cases of FeLV-A infection alone. The X region containing FeLV was discovered in two new cases. This study may elucidate the mechanism underlying FeLV-B-induced diseases.

microbiology↗

bioRxiv2024

Identifying Genetic Variations in emm89 Streptococcus pyogenes Linked to Severe Invasive Infections

Streptococcus pyogenes causes mild human infections as well as life-threatening invasive diseases. Since the mutations known to enhance virulence to date account for only half of the severe invasive infections, additional mechanisms/mutations need to be identified. Here, we conducted a genome-wide association study of emm89 S. pyogenes strains to comprehensively identify pathology-related bacterial genetic factors (SNPs, indels, genes, or k-mers). Japanese (n=311) and global (n=666) cohort studies of strains isolated from invasive or non-invasive infections revealed 17 and 1,075 SNPs/indels and 2 and 169 genes, respectively, that displayed associations with invasiveness. We validated one of them, a non-invasiveness-related point mutation, fhuB T218C, by structure predictions and introducing it into a severe invasive strain and confirmed that the mutant showed slower growth in human blood. Thus, we report novel mechanisms that convert emm89 S. pyogenes to an invasive phenotype and a platform for establishing novel treatments and prevention strategies.

microbiology↗

bioRxiv2024

A large attachment organelle mediates interaction between a novel Nanobdellota archaeon YN1 and its host

DPANN archaea are an enigmatic superphylum that are difficult to isolate and culture in the laboratory due to their specific culture conditions and apparent ectosymbiotic lifestyle. Here we successfully isolated and cultivated a co-culture system of a novel Nanobdellota archaeon YN1 and its host Sulfurisphaera ohwakuensis YN1HA. We characterised the co-culture system by complementary methods, including metagenomics and metabolic pathway analysis, fluorescence microscopy, and high-resolution electron cryo-tomography (CryoET). We show that YN1 is deficient in essential metabolic processes and requires host resources to proliferate. CryoET imaging revealed an enormous attachment organelle present in the YN1 envelope that forms a direct interaction with the host cytoplasm, bridging the two cells. Together our results unravelled the molecular and structural basis of ectosymbiotic relationship between YN1 and YNHA. This research broadens our understanding of DPANN biology and the versatile nature of their ectosymbiotic relationships.

microbiology↗

bioRxiv2024

Diurnal regulation of SOS Pathway and Sodium Excretion Underlying Salinity Tolerance of Vigna marina

Vigna marina (Barm.) Merr. is adapted to tropical marine beaches and has an outstanding tolerance to salt stress. Given there are growing demands for cultivating crops in saline soil or with saline water, it is important to understand how halophytic species are adapted to the saline environments. Here we revealed by positron emitting tracer imaging system (PETIS) that V. marina actively excretes sodium from the root during the light period but not in the dark period. The following whole genome sequencing accompanied with forward genetic study identified a QTL region harboring SOS1, encoding plasma membrane Na+/H+ antiporter, which was associated with not only salt tolerance but also ability of sodium excretion. We also found the QTL region contained a large structural rearrangement that suppressed recombination across [~]20 Mbp, fixing multiple gene loci potentially involved in salt tolerance. RNA-seq and promoter analyses revealed SOS1 in V. marina was highly expressed even without salt stress and its promoter shared common cis-regulatory motifs with those exhibiting similar expression profile. Interestingly, the cis-regulatory motifs seemed installed by a transposable element (TE) insertion. Though not identified by genetic analysis, the transcriptome data also revealed SOS2 transcription was under diurnal regulation, explaining the pattern of sodium excretion together with up-regulated expression of SOS1. Furthermore, we demonstrated that, under a condition of mild salt stress, the plants with the diurnally regulated SOS pathway outperformed those with the constitutively activated one.

plant biology↗

bioRxiv2023

The androgen receptor in mesenchymal progenitors regulates skeletal muscle mass via Igf1 expression in male mice.

Androgens exert their effects primarily by binding to the androgen receptor (AR), a ligand-dependent nuclear receptor. While androgens have anabolic effects on skeletal muscle, previous studies reported that AR functions in myofibers to regulate skeletal muscle quality, rather than skeletal muscle mass. Therefore, the anabolic effects of androgens are exerted via extra-myofiber cells or tissues. In this context, the cellular and molecular mechanisms of AR in mesenchymal progenitors, which play a crucial role in maintaining skeletal muscle homeostasis, remain largely unknown. In this study, we demonstrated expression of AR in mesenchymal progenitors and found that targeted AR ablation in mesenchymal progenitors reduced limb muscle mass in mature adult, but not young or aged, male mice, although fatty infiltration of muscle was not affected. The absence of AR in mesenchymal progenitors led to remarkable perineal muscle hypotrophy, regardless of age, due to abnormal regulation of transcripts associated with cell death and extracellular matrix organization. Additionally, we revealed that AR in mesenchymal progenitors regulates the expression of insulin-like growth factor 1 (Igf1), and that IGF1 administration prevents perineal muscles atrophy in a paracrine manner. These findings indicate that the anabolic effects of androgens regulate skeletal muscle mass via, at least in part, AR signaling in mesenchymal progenitors. Significance statementAndrogens are essential not only for the development of male sexual characteristics but also for a range of physiological functions, including the regulation of skeletal muscle growth and function. Understanding the functionality of the androgen receptor (AR) is essential for comprehending the mechanisms through which androgens exert their effects on skeletal muscles, as these effects are mediated through AR binding. We demonstrate that AR is expressed in mesenchymal progenitors, which play a vital role in muscle homeostasis, and regulates the expression of insulin-like growth factor 1 (Igf1)--a key player in skeletal muscle growth--to control muscle mass. Our study provides significant insights into potential therapeutic strategies for addressing muscle atrophy conditions like sarcopenia.

molecular biology↗

bioRxiv2023

A single-cell atlas of transcribed cis-regulatory elements in the human genome

Transcribed cis-regulatory elements (tCREs), such as promoters and enhancers, are fundamental to modulate gene expression and define cell identity. The detailed mapping of tCREs at single-cell resolution is essential for understanding the regulatory mechanisms that govern cellular functions. Prior tCRE catalogs, limited by bulk analysis, have often overlooked cellular heterogeneity. We have constructed a tCRE atlas using single-cell 5-RNA-seq, capturing over 340,000 single-cells from 23 human tissues and annotating more than 175,000 tCREs, substantially enhancing the scope and granularity of existing cis-regulatory element annotations in the human genome. This atlas unveils patterns of gene regulation, revealing connections between broadly expressed promoters and cell type-specific distal tCREs. Assessing trait heritability at single-cell resolution with a novel tCRE module-based approach, we uncovered the nuanced trait-gene regulatory relationships across a continuum of cell populations, offering insights beyond traditional gene-level and bulk-sample analyses. Our study bridges the gap between gene regulation and trait heritability, underscoring the potential of single-cell analysis to elucidate the genetic foundations of complex traits. These insights set the stage for future research to investigate the impact of genetic variations on diseases at the individual level, advancing the understanding of cellular and molecular basis of trait heritability.

genomics↗

bioRxiv2022

Genome sequence of 12 Vigna species as a knowledge base of stress tolerance and resistance

Harnessing plant genetic resources including wild plants enables exploitation of agronomically unfavorable lands to secure food in the future. The genus Vigna, family Fabaceae, consists of many species of such kind, as they are often adapted to harsh environments including marine beach, arid sandy soil, acidic soil, limestone karst and marshes. Here we report long-read assemblies of 12 Vigna species, achieving 95% or higher BUSCO scores. The comparative analyses discovered a new class of WUSCHEL-related homeobox (WOX) transcription factor superfamily that are incorporated into LTR retrotransposons and have dramatically amplified in some species of the genus Vigna. Except WOX transcription factors, however, gene contents are highly conserved among Vigna species with few copy number variations. On the other hand, transcriptome data provided some insights that transcriptional alterations played more important roles in evolution of stress tolerance in the genus Vigna. The whole genome sequences presented in this study will facilitate understanding genetic mechanisms of stress tolerance and application for developing new crops that are adapted to unfavorable environments.

genomics↗

bioRxiv2021

Uhrf1 governs the proliferation and differentiation of muscle satellite cells

DNA methylation is an essential form of epigenetic regulation responsible for cellular identity. In muscle stem cells, termed satellite cells, DNA methylation patterns are tightly regulated during differentiation. However, it is unclear how these DNA methylation patterns are maintained. We demonstrate that a key epigenetic regulator, ubiquitin like with PHD and RING finger domains 1 (Uhrf1), is activated in proliferating myogenic cells but not expressed in quiescent or differentiated myogenic cells in mice. Ablation of Uhrf1 in mouse satellite cells impairs their proliferation and differentiation, leading to failed muscle regeneration. Loss of Uhrf1 in satellite cells alters transcriptional programs, leading to DNA hypomethylation with activation of Cdkn1a and Notch signaling. Although down-regulation of Cdkn1a rescued proliferation but not differentiation, inhibition of Notch signaling rescued impaired differentiation of Uhrf1-deficient satellite cells. These findings point to Uhrf1 as a regulator of self-renewal and differentiation of satellite cells via genome-wide DNA methylation patterning.

molecular biology↗

bioRxiv2021

Identifying Brain Regions Related to Word Prediction During Listening to Japanese Speech by Combining a LSTM Language Model and MEG

Recently, a neuroscientific approach has revealed that humans understand language while subconsciously predicting the next word from the preceding context. Most studies on human word prediction have investigated the correlations between brain activity while reading or listening to sentences on functional magnetic resonance imaging (fMRI) and the predictive difficulty of each word in a sentence calculated by the N-gram language model. However, because of its low temporal resolution, fMRI is not optimal for identifying the changes in brain activity that accompany language comprehension. In addition, the N-gram language model is a simple computational structure that does not account for the structure of the human brain. Furthermore, it is necessary for humans to retain information prior to the N-1 word in order to form a contextual understanding of a presented story. Therefore, in the present study, we measured brain activity using magnetoencephalography (MEG), which has a higher temporal resolution than fMRI, and calculated the prediction difficulty of words using a long short-term memory language model (LSTMLM), which is based on a neural network inspired by the structure of the human brain and has longer information retention than the N-gram language model. We then identified the brain regions involved in language prediction during Japanese-language speech listening using encoding and decoding analyses. In addition to surprisal-related regions revealed in previous studies, such as the superior temporal gyrus, fusiform gyrus, and temporal pole, we also found relationships between surprisal and brain activity in other regions, including the insula, superior temporal sulcus, and middle temporal gyrus, which are believed to be involved in longer-term, sentence-level cognitive processing.

neuroscience↗