Biology subjects

Taniguchi, T.

Publications and source records attributed to Taniguchi, T..

10 recordsLinked to original sources

bioRxiv2026

BRCA2 loss triggers a downward spiral of genomic instability via ROS-dependent metabolic collapse

BRCA2 plays a central role in maintaining genome integrity through homologous recombination and replication-fork protection, yet the compensatory networks sustaining BRCA2-deficient cells remain unclear. Here we show BRCA2 enforces a homeostatic mechanism aligning mitochondrial respiration with DNA repair capacity in both cancer and non-cancer contexts. Genome-wide CRISPR screening identified glutathione metabolism and base-excision repair as the key compensatory networks sustaining BRCA2-deficient cells by detoxifying mitochondria-derived reactive oxygen species. BRCA2 loss provokes an acute mitochondrial ROS surge, causing 8-oxoguanine accumulation and a systemic metabolic crisis marked by NAD+ and glutathione depletion. PARP inhibitor targets DNA replication vulnerabilities, increasing the cellular requirement for BRCA2. The resulting oxidative burden primes cells for TP53-dependent apoptosis in G1 during olaparib treatment, which extends cytotoxicity beyond canonical S-phase stress. These findings indicate BRCA2 prevents metabolic flux from outpacing repair capacity, providing a rationale for combining PARP inhibition with redox modulation to enhance efficacy and overcome resistance. HighlightsO_LIAcute BRCA2 loss induces ROS and mitochondrial dysfunction creating a metabolic scar C_LIO_LIOxidative lesions drive PARP hyperactivation and precipitate a cellular NAD crisis C_LIO_LIPARP inhibitors provoke TP53-dependent apoptosis in G1 beyond replication stress in S phase C_LIO_LIGlutathione deficiency exacerbates bone marrow failure under BRCA2 depletion C_LIO_LIBRCA2 tightly couples mitochondrial redox homeostasis to genomic maintenance C_LI

cell biology↗

bioRxiv2025

Evolution towards higher unitary conductance in mammals makes BK channels more efficient and precise

The large conductance calcium-activated potassium channel, known as the BK channel, play an essential role in neuronal firing and is characterized by a very large [~]250pS unitary conductance in mammals. However, this high unitary conductance is not consistent across all species with invertebrates demonstrating a much lower unitary conductance. We explored the calcium activation properties of BK channels of different unitary conductance in computational models and found that mammalian channels are more efficiently activated by calcium and produce a stronger potassium current compared to the channels of lower unitary conductance found in invertebrates. The lower unitary conductance channels display fierce competition for the available calcium, which results in low activation and weaker current. Due to these properties, mammalian BK channels are more suitable to repolarize sodium action potentials, which enables more precise spike timing, and may explain why evolution appears to have favored a trend towards very high unitary conductance in mammalian BK channels. This may be an essential component of the more advanced brain functions achieved by these species compared to invertebrates.

neuroscience↗

bioRxiv2025

Field potential Imaging in human iPSC- derived Cardiomyocytes using UHD-CMOS-MEA

Evaluation using beat propagation analysis of human iPS cardiomyocytes is an effective approach for assessing human cardiac safety in drug development. However, current applications are primarily focused on detecting QT prolongation and arrhythmia risk, while its ability to comprehensively detect cardiotoxicity remains insufficient. Additionally, predicting the mechanism of action, which is crucial in drug development, remains challenging. In this study, we employed field potential imaging (FPI) using an ultra-high-density (UHD) CMOS microelectrode array (MEA) comprising 236,880 electrodes with high spatiotemporal resolution, capable of recording the activity of a monolayer of cardiomyocytes with tens of electrodes per cell. This method enabled the establishment of novel electrophysiological endpoints, including the number of excitation origins, fluctuations in origin positions, conduction velocity, and propagation area. Pharmacological characterization revealed drug-specific effects: isoproterenol increased excitation origins, mexiletine reduced conduction velocity, and E-4031 decreased propagation area while inducing early afterdepolarizations. Multivariate analysis of 13 compounds across 17 electrophysiological endpoints distinguished conduction velocity and propagation patterns based on their mechanisms of action. Additionally, 0.1 M doxorubicin exposure for 24 hours significantly reduced conduction velocity and propagation area, allowing early detection of chronic cardiotoxicity. These findings suggest that UHD-CMOS-MEA-based FPI enhances cardiotoxicity detection at low concentrations and precisely characterizes ion channel activity across different drug concentrations. The integration of novel electrophysiological endpoints derived from UHD-CMOS-MEA-based FPI, including excitation origin analysis, conduction velocity, and propagation area, along with multivariate analysis, is anticipated to establish a next-generation in vitro platform for comprehensive cardiotoxicity risk assessment and mechanism-based prediction of drug candidates.

pharmacology and toxicology↗

bioRxiv2025

Conserved metabolic adaptation mechanisms in cancer cells and yeast against mitochondrial dysfunction indicate an additional role of aerobic glycolysis for cell survival

Eukaryotic cells primarily generate ATP through oxidative phosphorylation and substrate-level phosphorylation. Despite the superior efficiency of oxidative phosphorylation, eukaryotic cells often utilize both pathways as aerobic glycolysis even in the presence of oxygen. However, its role in cell survival remains poorly understood. In this study, aerobic glycolysis of the Warburg effect in breast cancer cells (MCF7) and the Crabtree effect in a laboratory strain of Saccharomyces cerevisiae (S288C) were compared following treatment with electron transport chain inhibitors, including FCCP, antimycin A, and oligomycin. MCF7 and S288C exhibited strikingly similar metabolic rewiring toward substrate-level phosphorylation against the inhibitor treatment, suggesting that mitochondrial oxidative phosphorylation and cytosolic substrate-level phosphorylation communicate through a common mechanism. Measurements of mitochondrial membrane potential (MMP) and ATP concentration further indicated that cytosolic ATP was transported into the mitochondria under conditions of reduced electron transport chain activity. This ATP was likely utilized by the reverse mode of H+/ATPase to maintain the MMP which contributed to avoiding programmed cell death. These results suggest that the ATP supply to mitochondria plays a conserved role in aerobic glycolysis across yeast and mammalian cancer cells. This mechanism likely contributes to cell survival under conditions of fluctuating oxygen availability.

cell biology↗

bioRxiv2024

The Rubicon-WIPI axis regulates exosome biogenesis during aging

Cells release intraluminal vesicles (ILVs) in multivesicular bodies as exosomes to communicate with other cells. Although recent studies suggest an intimate link between exosome biogenesis and autophagy, the detailed mechanism is not fully understood. Here we employed comprehensive RNAi screening for autophagy-related factors and discovered that Rubicon, a negative regulator of autophagy, is essential for exosome release. Rubicon recruits WIPI2d to endosomes to promote exosome biogenesis. Interactome analysis of WIPI2d identified the ESCRT components that are required for ILV formation. Notably, we found that Rubicon is required for an age-dependent increase of exosome release in mice. In addition, small RNA sequencing of serum exosomes revealed that Rubicon determines the fate of exosomal microRNAs associated with cellular senescence and longevity pathways. Taken together, our current results suggest that the Rubicon-WIPI axis functions as a key regulator of exosome biogenesis and is responsible for the age-dependent changes in exosome quantity and quality.

cell biology↗

bioRxiv2023

Diffusion of DNA on Atomically Flat 2D Material Surfaces

Accurate localization of biomolecules is pivotal for understanding biological processes. Utilizing the atomically flat surface of 2D materials offers a promising route to achieve this without the need for tethering or constraining. Here we comprehensively investigate the binding and diffusion of DNA on hexagonal boron nitride (hBN) surfaces. Our findings reveal non-specific binding of DNA to pristine hBN, with subsequent diffusion and confinement within the 2D plane. Through single-molecule experiments and computational techniques, we explore DNA dynamics, and the effects of defects, step edges and domain boundaries on the motion, which gives insights on the interactions between solid-state surfaces and biomolecules. By engineering a narrow hBN ribbon structure, we enhance confinement, demonstrating its potential in nanofluidic guiding of biomolecules. Our 2D platform serves as a proving ground for next generation high-throughput single-molecule manipulation techniques for enabling applications in biotechnology and nanotechnology.

molecular biology↗

bioRxiv2023

Critical capillary waves of biomolecular condensates

Biomolecular condensates formed by phase separation are key players in cellular organization, yet their interfacial mechanics remain poorly understood. Here, we show that both synthetic and endogenous nuclear condensates exhibit critical-like interfacial behaviors near the phase boundary, including enhanced capillary fluctuations, critical slowing down, and reduced surface tension. By combining optogenetic control with sub-micron-resolution fluctuation spectroscopy, we quantitatively estimate surface tension, bending rigidity, and effective viscosity. Surface tension diminishes as the system approaches the critical composition, consistent with classical theories of phase separation. Notably, bending elasticity emerges as an unexpected feature of these nuclear liquid-like structures, suggesting the formation of structured interfacial layers that progressively weaken near criticality. Among these condensates, the nucleolus displayed exceptionally high viscosity, which may arise in part from viscoelastic coupling to the surrounding perinucleolar heterochromatin, effectively increasing the apparent viscosity in the long-time fluctuation regime. This non-invasive approach enables probing condensate mechanics in living cells and may provide a basis for diagnosing or modulating condensates in biomedical contexts.

biophysics↗

bioRxiv2023

CRISPR/Cas9-mediated disruption of CjACOS5 confers no-pollen formation on sugi trees (Cryptomeria japonica D. Don)

Sugi (Cryptomeria japonica D. Don) is an economically important coniferous tree in Japan. However, abundant sugi pollen grains are dispersed and transported by the wind each spring and cause a severe pollen allergy syndrome (Japanese cedar pollinosis). The use of pollen-free sugi that cannot produce pollen has been thought as a countermeasure to Japanese cedar pollinosis. The sugi CjACOS5 gene is an ortholog of Arabidopsis ACOS5 and rice OsACOS12, which encode an acyl-CoA synthetase that is involved in the synthesis of sporopollenin in pollen walls. To generate pollen-free sugi, we mutated CjACOS5 using the CRISPR/Cas9 system. As a result of sugi transformation mediated by Agrobacterium tumefaciens harboring the CjACOS5-targeted CRISPR/Cas9 vector, 1 bp-deleted homo biallelic mutant lines were obtained. Chimeric mutant lines harboring both mutant and wild-type CjACOS5 genes were also generated. The homo biallelic mutant lines had no-pollen in male strobili, whereas chimeric mutant lines had male strobili with or without pollen grains. Our results suggest that CjACOS5 is essential for the production of pollen in sugi and that its disruption is useful for the generation of pollen-free sugi. In addition to conventional transgenic technology, genome editing technology, including CRISPR/Cas9, can confer new traits on sugi.

plant biology↗

bioRxiv2022

Germinal center-derived broadly neutralizing antibodies adapt to SARS-CoV-2 antigenic drift

The outbreak of SARS-CoV-2 variant Omicron which harbors a striking number of mutations in the spike protein has been raising concerns about the effectiveness of vaccines and antibody treatment1. Here, we confirmed a substantial reduction in neutralizing potency against Omicron in all convalescent and vaccinated sera. However, we found that some people infected by the early strain show relatively higher neutralization to Omicron. From those B cells, we developed neutralizing antibodies inhibiting broad variants including Delta and Omicron. Unlike reported antibodies, one had an extremely large interface and widely covered receptor binding motif of spike, thereby interfering with diversified variants. Somatic mutations introduced by long-term germinal center reaction contributed to the key structure of antibodies and the universal interaction with spike variants. Recalling such rare B cells may confer sustainable protection against SARS-CoV-2 variants emerging one after another.

immunology↗

bioRxiv2020

Therapeutic Efficacy and Safety of Lenvatinib for Unresectable Hepatocellular Carcinoma Beyond Progression with Sorafenib

Background & AimsThe efficacy and safety of lenvatinib (LEN) as a second/third-line treatment for unresectable hepatocellular carcinoma (HCC) after sorafenib (SOR) therapy remains unknown. We evaluated the outcomes of second/third-line treatment of LEN, investigated the sensitivity of SOR-resistant HCC cell line (PLC/PRF5-R2) to LEN, and their signal transduction pathway by protein array analysis. MethodsWe retrospectively enrolled 57 unresectable HCC patients. Radiologic responses in 53 patients were evaluated by modified Response Evaluation Criteria in Solid Tumors. Active signal transduction pathways in cells were identified by protein array analysis, including 1205 proteins. ResultsPatients comprised 34 tyrosine kinase inhibitor (TKI)-naive (first-line), nine SOR-intolerant (second-line), and ten resistant to regorafenib (third-line). Objective response rates (ORRs) were 61.8% (21/34) in TKI-naive, 33.3% (3/9) in second-line, and 20.0% (2/10) in third-line groups. The overall survival (OS) and the progression free survival (PFS) in the first-line was significantly longer than those in third-line group (p<0.05). Patients with better liver functional reserve (Child score, ALBI grade) exhibited higher ORR and longer OS. LEN was well-tolerated as second/third-line treatment. The IC50 value of LEN against PLC/PRF5-R2 cells (30 M) was significantly higher than that against PLC/PRF5 cells (6.4 M). LEN inhibited significantly more signal transduction pathways related to FRS2, a crucial FGFR downstream molecule, in PLC/PRF5 than PLC/PRF5-R2 cells. ConclusionsLEN was active and safe as a second/third-line treatment for unresectable HCC. LEN seems to be more effective for HCC patients with better hepatic reserve function or before TKI-resistance is acquired because of partial cross-resistance to SOR.

molecular biology↗