Biology subjects

Ishibashi, T.

Publications and source records attributed to Ishibashi, T..

14 recordsLinked to original sources

bioRxiv2026

Force transmission balance through adhesions determines multicellular handedness

Cell chirality has been implicated in left-right (LR) asymmetric morphogenesis, yet multicellular handedness is not a simple readout of single-cell chirality. Here, we show that multicellular LR asymmetry is determined by the balance of force transmission through cell-cell and cell-substrate adhesions. Combining experiments in human epithelial cells with theoretical modeling, we demonstrate that clockwise-rotating single cells can generate either clockwise or counterclockwise collective rotation depending on whether chiral forces are transmitted primarily through adherens junctions or focal adhesions, without altering single-cell chirality itself. Mechanistically, microtubules promoted junctional force transmission by recruiting the actin-microtubule crosslinker ACF7 to cell-cell contacts, where ACF7 stabilized F-actin and enabled intercellular mechanical coupling. Our results define a mechanical framework in which the routing of chiral forces through adhesions, rather than single-cell chirality alone, determines multicellular handedness.

cell biology↗

bioRxiv2026

gSV: a general structural variant detector using the third-generation sequencing data

Structural variants (SVs) are major contributors to genome diversity and disease susceptibility, particularly in cancer. Although third-generation sequencing technologies have substantially improved SV detection sensitivity, accurate detection of complex SVs remains challenging due to fragmented and heterogeneous alignment signals, as well as the dependence of many existing methods on predefined variant models. In this paper, we propose gSV, a general SV detector that integrates alignment-based and assembly-based approaches with the maximum exact match (MEM) strategy, with particular emphasis on resolving SVs with complex or atypical alignment signatures. Without predefined assumptions about SV types, gSV captures diverse variant signals, enabling the detection of SVs that are usually missed by conventional tools. Benchmarking using both simulated datasets and real long-read sequencing data demonstrates that gSV achieves improved sensitivity and overall detection performance compared with current state-of-the-art SV callers, particularly for simple and complex SV events with complex alignment patterns. Unique SV discoveries in four breast cancer cell lines, particularly in cancer-associated genes, demonstrate the potential biological relevance of gSV-enabled discoveries. Furthermore, analysis of a breast cancer cohort from the Chinese population highlights the utility of gSV for population-scale genomic studies. Collectively, gSV provides a unified framework for comprehensive SV discovery in both research and clinical genomics settings. O_TEXTBOXKey PointsO_LIExisting structural variant (SV) detection tools are limited in resolving SVs with complex alignment patterns due to their reliance on predefined variant models. C_LIO_LIgSV integrates alignment-based and assembly-based evidence using a maximum exact match (MEM) strategy, enabling capture of diverse and complex SV signals. C_LIO_LIBenchmarking on simulated and real long-read sequencing datasets demonstrates that gSV achieves competitive performance on canonical SV classes and improved sensitivity for complex SV patterns. C_LIO_LIApplication of gSV to breast cancer cell lines and a population-scale breast cancer cohort reveals previously unresolved SVs in cancer-associated genes, highlighting its utility in genomic and clinical studies. C_LI C_TEXTBOX

bioinformatics↗

bioRxiv2024

Epigenetic reprogramming induced by Acetyl-CoA and SAM depletion is an evolutionarily-ancient path to malignant growth

Despite the vast diversity of life forms and living histories, it appears that all branches of Metazoa face the challenge of tumor growth. Contrary to human tumors, which take years to form, tumors in short-living species can arise within days without accumulating multiple mutations, raising the question whether the paths to tumorigenesis in diverse species have any commonalities. In a fly tumor model caused by loss of cell polarity genes, we first identified the rise of a glycolytic cell population over time, resembling the Wartburg effect observed in human tumors. We further identified two key metabolic changes in these fly tumors. First, a systemic depletion of acetyl-CoA leads to a reduction in histone acetylation levels and stochastic silencing of actively-transcribed genes. Second, defects in the methionine cycle cause a systemic depletion of S-Adenosyl methionine, which further reduces histone methylation levels and causes stochastic activation of transposons. Perturbation of the methionine metabolic process strongly inhibits tumor growth. Finally, to understand the evolutionary origin of tumorigenesis, we performed comparative studies of fly and human tumors, and identified human tumors that exhibit metabolic signatures similar to those of fly tumors. We found that human tumors with high metabolic similarity to fly tumors have a lower mutational load, younger patient age, and lower DNA methylation levels. This study suggests that tumorigenesis processes have a deep evolutionary origin and highlights that depletion of key metabolites is an evolutionarily-ancient driving force for tumorigenesis.

developmental biology↗

bioRxiv2024

H2B.W2, a Spermatocytes-specific Histone Variant, disrupts nucleosome stability and reduces chromatin compaction

Spermatogenesis is a highly regulated process that requires precise chromatin remodeling, which includes the incorporation of testis-specific histone variants. While several of these variants have been characterized, the role of H2B.W2, a member of the H2BW family, remains largely unclear. Here, we showed that H2B.W2 expression occurs mainly in spermatocytes, slightly later than its paralog H2B.W1. Cryo-electron microscopy (cryo-EM) analysis of H2B.W2-containing nucleosomes reveals a more relaxed conformation compared to canonical nucleosomes caused by weakened interactions between the outer DNA turn and the histone core. We pinpointed the N-terminal tail and 2 helix of H2B.W2, specifically residues D85 and Q101, as critical for nucleosome destabilization. Furthermore, we identify G73 within the L1 loop as a key residue involved in disrupting higher-order chromatin structure. Our findings suggest that H2B.W2-mediated nucleosome and chromatin destabilization may play a role in regulating gene expression during spermatogenesis, with potential implications for sperm development and function.

biochemistry↗

bioRxiv2024

Applying gradient tree boosting to QTL mapping with Shapley additive explanations

Mapping quantitative trait loci (QTLs) is one of the major goals of quantitative genetics; however, identifying the interactions between QTLs (i.e., epistasis) remains challenging. Recently developed machine learning methods, such as deep learning and gradient boosting, are transforming the real world. These methods could advance QTL mapping methodologies because of their high capability for capturing complex relationships among features. One problem with applying such complex models to QTL mapping is the evaluation of feature importance. In this study, XGBoost, a popular gradient tree boosting algorithm, was applied for QTL mapping in biparental populations with Shapley additive explanations (SHAPs). SHAP is a local (i.e., instance-wise) importance index with the desired properties as feature importance indices. The SHAP-assisted XGBoost (SHAP-XGB) was compared with conventional methods, including composite interval mapping (CIM), multiple interval mapping (MIM), inclusive CIM (ICIM), and BayesC, using simulations and rice heading date data. SHAP-XGB performed comparablely to CIM, MIM, ICIM, and BayesC in mapping main QTL effects and was superior to MIM, ICIM, and BayesC in mapping QTL interaction effects. As SHAP can evaluate local importance, interactions between markers can be visualized by plotting SHAP interaction values for each instance (plant/line). These results illustrated the strength of SHAP-XGB in detecting and interpreting epistatic QTLs and suggest the possibility that SHAP-XGB complements conventional methods.

genetics↗

bioRxiv2023

Epithelial cell chirality emerges through the dynamic concentric pattern of actomyosin cytoskeleton

The chirality of tissues and organs is essential for their proper function and development. Tissue-level chirality derives from the chirality of individual cells that comprise the tissue, and cellular chirality is considered to emerge through the organization of chiral molecules within the cell. However, the principle of how molecular chirality leads to cellular chirality remains unresolved. To address this fundamental question, we experimentally studied the chiral behaviors of isolated epithelial cells derived from a carcinoma line and developed a theoretical understanding of how their behaviors arise from molecular-level chirality. We first found that the nucleus rotates and the cytoplasm circulates robustly in a clockwise direction. During the rotation, actin and myosin IIA are organized into stress fibers with a vortex-like chiral orientation at the ventral side of the cell periphery, simultaneously forming thin filaments with a concentric orientation at the dorsal level of the cell. Surprisingly, we found that the intracellular rotation is driven by the concentric pattern of actomyosin filaments on the dorsal surface of the cell, not by the vortex-like chiral stress fibers. To elucidate how the concentric actomyosin filaments induce chiral rotation, we analyzed a theoretical model developed based on the theory of active chiral fluid, and revealed that the observed cell-scale unidirectional rotation is driven by the molecular-scale chirality of actomyosin filaments even in the absence of cell-scale chiral orientational order. Our study thus provides novel mechanistic insights into how the molecular chirality is organized into the cellular chirality and an important step towards understanding left-right symmetry breaking in tissues and organs.

cell biology↗

bioRxiv2022

FDA-approved drug screening identified micafungin as an antiviral agent against bat-borne emerging zoonotic Pteropine orthoreovirus

Bat-borne emerging zoonotic viruses cause major outbreaks, such as the Ebola virus, Nipah virus, severe acute respiratory syndrome (SARS) coronavirus, and SARS-CoV-2. Pteropine orthoreovirus (PRV), which spillover event occurred from fruit bats to humans, causes respiratory syndrome in humans widely in South East Asia. Repurposing approved drugs against PRV is a critical tool to confront future PRV pandemics. We screened 2,943 compounds in an FDA-approved drug library and identified eight hit compounds that reduce viral cytopathic effects on cultured Vero cells. Real-time quantitative PCR analysis revealed that six of eight hit compounds significantly inhibited PRV replication. Among them, micafungin used clinically as an antifungal drug, displayed a prominent antiviral effect on PRV. HighlightsO_LIA library of 2,943 FDA-approved drugs was screened to find potential antiviral drugs of Pteropine orthoreovirus. C_LIO_LISix hit compounds dramatically inhibited viral replication in vitro. C_LIO_LIMicafungin possessed antiviral activity to multiple strains of PRV. C_LI

pharmacology and toxicology↗

bioRxiv2022

The Drosophila AWP1 ortholog Doctor No regulates JAK/STAT signaling for left-right asymmetry in the gut by promoting receptor endocytosis

Many internal Drosophila organs show stereotypical left-right (LR) asymmetry, for which the underlying mechanisms remain elusive. Here, we identified an evolutionarily conserved ubiquitin-binding protein, AWP1/Doctor no (Drn), as a novel factor required for the LR asymmetry of the embryonic anterior gut in Drosophila. We showed that drn is essential in the circular visceral muscle cells of the midgut for JAK/STAT signaling, which contributes to the first known cue for anterior gut lateralization via LR-asymmetric nuclear rearrangement. Embryos homozygous for drn and lacking its maternal contribution showed phenotypes similar to that of depleted JAK/STAT signaling, suggesting that Drn is a general component of JAK/STAT signaling. The absence of Drn resulted in the specific accumulation of Domeless (Dome), the receptor of JAK/STAT signaling, in intracellular compartments. Thus, Drn is required for the endocytic trafficking of Dome, which is subsequently degraded in lysosomes. Our results suggest that the endocytosis of Dome is a critical step in activating JAK/STAT signaling. The roles of AWP1/Drn in activating JAK/STAT signaling and in LR-asymmetric development may be conserved in various organisms. Summary StatementDr. No, a Drosophila ortholog of AWP1, activates JAK/STAT signaling via Dome receptor endocytosis in a crucial step for left-right asymmetry in the developing gut.

developmental biology↗

bioRxiv2022

Testis-specific H2BFWT disrupts nucleosome integrity through reductions of DNA-histone interactions

During spermatogenesis, multiple testis-specific histone variants are involved in the dynamic chromatin transitions. H2BFWT is a primate testis-specific H2B variant with hitherto unclear functions, and SNPs of H2BFWT are closely associated with male non-obstructive infertility. Here, we found that H2BFWT is preferentially localized in the sub-telomeric regions and the promoters of genes highly expressed in testis from differentiated spermatogonia to early spermatocytes. Cryo-EM structural analysis shows that H2BFWT nucleosomes are defined by weakened interactions between H2A-H2BFWT dimer and H4, and between histone octamer and DNA. Furthermore, one of its SNPs, H2BFWTH100R further destabilizes nucleosomes and increases the nucleosome unwrapping rate by interfering with the interaction with H4K91. Our results suggest that H2BFWT may be necessary for the regulation of spermatogenesis-related gene expression by decreasing transcriptional barriers, and that H2BFWTH100R overdrives its nucleosome-destabilizing effects which causes infertility.

biochemistry↗

bioRxiv2021

Bisphenol A derivatives act as novel coactivator binding inhibitors for estrogen receptor β

Bisphenol A and its derivatives are recognized endocrine disruptors based on their complex effects on estrogen receptor (ER) signaling. While the effects of bisphenol derivatives on ER have been thoroughly evaluated, how these chemicals affect ER{beta} signaling is not well understood. Herein, we identified novel ER{beta} ligands by screening a chemical library of bisphenol derivatives. Many of the compounds identified showed intriguing dual activities as ER agonists and ER{beta} antagonists. Docking simulations suggested that these compounds act as coactivator binding inhibitors (CBIs). Direct binding experiments using wild-type and mutated ER{beta} demonstrated the presence of a second ligand interaction position at the coactivator binding site in ER{beta}. Our study is the first to propose that bisphenol derivatives act as CBIs, presenting a critical view point for future ER signaling-based drug development.

biochemistry↗

bioRxiv2020

Statistical validation verifies that enantiomorphic states of cell chirality are determinant dictating the left- or right-handed direction of the hindgut rotation in Drosophila

In the left-right (LR) asymmetric development of invertebrates, chirality of cells (cell chirality) plays crucial roles. Left- or right-handed structure of cells consequently directs the morphogenesis with corresponding LR asymmetry. In Drosophila, it has been suggested that cell chirality drives the LR-asymmetric development of various organs including the embryonic hindgut. However, this hypothesis is supported only by apparent concordance between these two events and by computer simulations connecting them [1-5]. Therefore, here, we mathematically evaluated the causal relationship between the cell chirality of the hindgut epithelial cells and the LR-directional rotation of the hindgut, which was previously postulated. Our logistic model obtained from various genetic backgrounds significantly explained the correlation between the enantiomorphic states of cell chirality and the LR directionality of hindgut rotation. This model also significantly explained the correlation between cell chirality stochastically formed in advance in each living embryo and the LR-directionality of the following rotation, suggesting the irrelevance of modes how cell chirality is formed. This analysis also showed that the cell chirality is not only sufficient but also required for the rotation. Considering the chronological order of these events, our study validated that cell chirality causally defines the LR asymmetry of the hindgut rotation.

developmental biology↗

bioRxiv2019

Systematic detection of Mendelian and non-Mendelian variants associated with retinitis pigmentosa by genome-wide association study

To uncover genetic basis of autosomal recessive retinitis pigmentosa (ARRP), we applied 2-step genome-wide association study (GWAS) in 640 Japanese patients prescreened with targeted re-sequencing. Meta-GWAS identified three independent peaks at P < 5.0x10-8, all within the major ARRP gene EYS. Two were each tagged by a low frequency variant (allele frequency < 0.05); a known founder Mendelian mutation (c.4957dupA, p.S1653Kfs*2) and a presumably hypomorphic non-synonymous variant (c.2528G>A, p.G843E). c.2528G>A newly solved 7.0% of Japanese ARRP cases, improving genetic diagnosis by 26.8% and simultaneously serving as a new attractive target for genome editing gene therapy. The third peak was tagged by an intronic common variant, representing a novel disease-susceptibility signal. GWAS successfully unraveled genetic causes of a rare "monogenic" disorder for the first time, which provided unexpected insights into significant contribution of non-Mendelian genetic factors and identified a novel high frequency variant directly linked to development of local genome therapeutics.

genetics↗

bioRxiv2018

A novel histone H4 variant regulates rDNA transcription in breast cancer

Histone variants, present in various cell types and tissues, are known to exhibit different functions. For example, histone H3.3 and H2A.Z are both involved in gene expression regulation, whereas H2A.X is a specific variant that responds to DNA double-strand breaks. In this study, we characterized H4G, a novel hominidae-specific histone H4 variant. H4G expression was found in a variety of cell lines and was particularly overexpressed in the tissues of breast cancer patients. H4G was found to localize primarily to the nucleoli of the cell nucleus. This localization was controlled by the interaction of the alpha helix 3 of the histone fold motif with the histone chaperone, nucleophosphomin 1. In addition, we found that H4G nucleolar localization increased rRNA levels, protein synthesis rates, and cell cycle progression. Furthermore, micrococcal nuclease digestion of H4G-containing nucleosomes reconstituted in vitro indicated that H4G destabilizes the nucleosome, which may serve to alter nucleolar chromatin in a way that enhances rDNA transcription in breast cancer tissues.

molecular biology↗

bioRxiv2018

Frequent variants in the Japanese population determine quasi-Mendelian inheritance of rare retinal ciliopathy

Hereditary retinal degenerations (HRDs) are Mendelian diseases characterized by progressive blindness and caused by ultra-rare mutations. In a genomic screen of 331 unrelated Japanese patients, we identify a disruptive Alu insertion and a nonsense variant (p.Arg1933*) in the ciliary gene RP1, neither of which are rare alleles in Japan. p.Arg1933* is almost polymorphic (frequency = 0.6%, amongst 12,000 individuals), does not cause disease in homozygosis or heterozygosis, and yet is significantly enriched in HRD patients (frequency = 2.1%, i.e. a 3.5-fold enrichment; p-value = 9.2x10-5). Familial co-segregation and association analyses show that p.Arg1933* can act as a Mendelian mutation, in trans with the Alu insertion, but might also cause disease in association with two alleles in the EYS gene in a non-Mendelian pattern of heredity. Our results suggest that rare conditions such as HRDs can be paradoxically determined by relatively common variants, following a quasi-Mendelian model linking monogenic and complex inheritance.

genomics↗