Biology subjects

Harada, T.

Publications and source records attributed to Harada, T..

16 recordsLinked to original sources

bioRxiv2026

Landscape of reversion alterations in homologous recombination genes reveals evolutionary constraints

Reversion mutations (REVs) restore homologous recombination repair (HRR) and confer resistance to PARP inhibitors (PARPi) in HR-deficient cancers. Yet, their prevalence, mechanisms, and biological constraints remain undefined. We analyzed genomic profiling of 609,464 tissue and liquid biopsy samples across multiple cancer types to delineate the pan-cancer landscape of REVs. REVs were identified in eight HRR genes, most frequently BRCA2 and BRCA1 and notably never in ATM or CHEK2. REVs exclusively impacted truncating pathogenic variants, predominantly through large in-frame and exon-level deletions, associated with repetitive sequences. Conserved functional domains are relatively depleted of REVs. Structural modeling and functional studies support that exon-level deletions preserve critical domain architecture and confer PARPi resistance. The study establishes HRR reversion as a structurally permissive, yet evolutionarily constrained, resistance mechanism with implications on response, monitoring, and therapeutic strategy. One Sentence SummaryHomologous recombination reversion evolves through structurally tolerated, microhomology-driven alterations that restore DNA repair under therapeutic selection across cancers.

cancer biology↗

bioRxiv2026

A practical pipeline for volume rendering of trillion-voxel tomographic data

Recent advancements in tomography produce imaging data of geological materials (rocks and fossils) at trillion-voxel scales with multi-channels. Such high-resolution datasets are potentially keys to unveil evolutionary biological information with various shapes and sizes that have not been ever discovered. Volume rendering is an ideal visualization approach for them because it treats all voxels without relying on user-defined surface boundaries. However, these large-scale real-world tomographic data have rarely been volume-rendered at their native resolution, limiting the examination of rich morphological information. Here, we demonstrate a de facto standard volume-rendering pipeline running on a graphical processing unit (GPU)-equipped supercomputing system toward multi-channel, trillion-voxel tomographic data. Our workflow preserves original resolution, capturing detailed morphological information spanning microscopic to macroscopic scales. Systematic comparison of node types shows that GPU memory, rather than host memory, is the primary bottleneck. Our results establish a baseline for large-scale, multi-channel volume rendering of real tomographic data and demonstrate its applicability to geological samples. This work is presented as a practical demonstration of large-scale volume visualization.

paleontology↗

bioRxiv2025

A nuclear branched-chain amino acid catabolism pathway controls histone propionylation in pancreatic cancer

Branched-chain amino acid (BCAA) catabolism contributes prominently to the TCA cycle in the healthy pancreas but is suppressed in pancreatic ductal adenocarcinoma (PDA). The impact of this metabolic remodeling on cancer phenotypes remains poorly understood. Here, we find that the BCAA isoleucine is a primary source of propionyl-CoA in PDA cells. Reduction of propionyl-CoA availability by either genetic perturbation or isoleucine and valine starvation decreases histone propionylation (Kpr) without impacting histone acetylation on specific lysine sites, correlating with reduced transcription of certain lipid- and immune-related genes. Mechanistically, we find that multiple enzymes of isoleucine catabolism unexpectedly localize to and carry out multi-step isoleucine oxidation within the nuclei of PDA cells. Importantly, nuclear localization of the rate-limiting branched-chain alpha ketoacid dehydrogenase (BCKDH) complex is essential for isoleucine-dependent Kpr and gene regulation. Moreover, we demonstrate that isoleucine-sensitive Kpr and its associated gene expression are driven by the MYST family of lysine acyltransferases (KATs), and that the BCKDHA subunit of the BCKDH complex interacts with KAT7 within the nuclear compartment. BCAA catabolism enzymes are apparent in the nuclei of PanIN lesions in mice and PDA tumors in patients, contrasting that in healthy pancreatic acinar and ductal cells. Collectively, these findings unveil a nuclear isoleucine catabolism pathway and highlight its role in controlling histone Kpr and tumorigenic transcriptional programs in PDA.

cancer biology↗

bioRxiv2025

Spectral acoustic contributions to musical pleasure are dynamically shaped by autonomic neural inputs

Most people enjoy music and often use music to regulate their emotions. Although pleasure derived from music-listening has been shown to be mediated by dopaminergic signals in the mesolimbic reward network, its relationship with physiology is still poorly understood. Here, we introduced time-warped representational similarity analysis (twRSA) to directly map dynamic representations of multiple modalities across variable-duration stimuli. Our method revealed that although time-varying spectral and tonal acoustic features predicted changes in autonomic neural responses (measured via cardiac, pupil, and respiratory activity) during music-listening, only a small subset was in fact relevant to listeners on-line pleasure ratings. Despite that, we identified a weak mediation effect of physiology on shaping musical pleasure. Our results thus indicate that whilst musical pleasure may be embodied in bodily responses, the mapping between subjective experience and physiology is likely one-to-many--in line with psychological construction theories of emotion--and not one-to-one as is commonly assumed in classical basic emotion theories.

neuroscience↗

bioRxiv2023

Rapid-kinetics degron benchmarking reveals off-target activities and mixed agonism-antagonism of MYB inhibitors

Attenuating aberrant transcriptional circuits holds great promise for the treatment of numerous diseases, including cancer. However, development of transcriptional inhibitors is hampered by the lack of a generally accepted functional cellular readout to characterize their target specificity and on-target activity. We benchmarked the direct gene-regulatory signatures of six agents reported as inhibitors of the oncogenic transcription factor MYB against targeted MYB degradation in a nascent transcriptomics assay. The inhibitors demonstrated partial specificity for MYB target genes but displayed significant off-target activity. Unexpectedly, the inhibitors displayed bimodal on-target effects, acting as mixed agonists-antagonists. Our data uncover unforeseen agonist effects of small molecules originally developed as TF inhibitors and argue that rapid-kinetics benchmarking against degron models should be used for functional characterization of transcriptional modulators.

molecular biology↗

bioRxiv2023

Leukemia core transcriptional circuitry is a sparsely interconnected hierarchy stabilized by incoherent feed-forward loops

Lineage-defining transcription factors form densely interconnected circuits in chromatin occupancy assays, but the functional significance of these networks remains underexplored. We reconstructed the functional topology of a leukemia cell transcription network from the direct gene-regulatory programs of eight core transcriptional regulators established in pre-steady state assays coupling targeted protein degradation with nascent transcriptomics. The core regulators displayed narrow, largely non-overlapping direct transcriptional programs, forming a sparsely interconnected functional hierarchy stabilized by incoherent feed-forward loops. BET bromodomain and CDK7 inhibitors disrupted the core regulators direct programs, acting as mixed agonists/antagonists. The network is predictive of dynamic gene expression behaviors in time-resolved assays and clinically relevant pathway activity in patient populations.

systems biology↗

bioRxiv2022

An antioxidant screen identifies ascorbic acid for prevention of light-induced mitotic prolongation in live cell imaging

Phototoxicity is an important issue in fluorescence live imaging of light-sensitive cellular processes such as mitosis, especially in high spatiotemporal resolution microscopy that often requires high-intensity illumination. Among several approaches to reduce phototoxicity, the addition of antioxidants to the imaging media has been used as a simple and effective method. However, it remains unknown what are the optimal antioxidants that could prevent phototoxicity-induced defects during mitosis in fluorescence live cell microscopy. In this study, we analyzed the impact of phototoxicity on the mitotic progression in fluorescence live imaging of human diploid cells and performed a screen to identify the most efficient antioxidative agents that reduce it. Quantitative analysis shows that high amounts of light illumination cause various mitotic defects such as prolonged mitosis and delays of chromosome alignment and centrosome separation. Among several antioxidants known to reduce cellular phototoxicity, our screen reveals that ascorbic acid significantly alleviates these phototoxic effects in mitosis. Furthermore, we demonstrate that the addition of ascorbic acid to the imaging media enables fluorescence imaging of mitotic events at very high temporal resolution without obvious photodamage. Thus, this study provides a simple and practical method to effectively reduce the phototoxic effects on mitotic processes in fluorescence live cell imaging.

cell biology↗

bioRxiv2022

Membrane-associated shortened Trk receptors promote neuroprotection and robust axon regeneration without ligands

Activation of neurotrophic factor signaling is a promising therapy for neurodegeneration. However, limited availability of both ligands and receptors permits only transient activation. In this study, we conquered this problem by inventing a new system that forces membrane localization of the intracellular domain of neurotrophin receptor TrkB, which results in constitutive activation without ligands. Our new system overcomes the small size limitation of the genome packaging in adeno-associated virus and allows high expression of the transgene. Single gene therapy using the modified form of TrkB enhances neuroprotection in mose models of glaucoma, and stimulates robust axon regeneration after optic nerve injury. Our system may be also applicable to other trophic factor signaling and lead to a significant advance in the field of gene therapy for neurodegenerative disorders.

neuroscience↗

bioRxiv2021

Neural basis for anxiety and anxiety-related physiological responses during simulated driving: An fMRI study

While the exteroceptive and interoceptive prediction of a negative event increases a persons anxiety in daily life situations, the relationship between the brain mechanism of anxiety and the anxiety-related autonomic response has not been fully understood. In this fMRI study, we examined the neural basis of anxiety and anxiety-related autonomic responses in a daily driving situation. Participants viewed a driving video clip in the first-person perspective. During the video clip, participants were presented with a cue to indicate whether a subsequent crash could occur (attention condition) or not (safe condition). Enhanced activities in the anterior insula, bed nucleus of the stria terminalis, thalamus, and periaqueductal gray, and higher sympathetic nerve responses (pupil dilation and peripheral arterial stiffness) were triggered by the attention condition but not with the safe condition. Autonomic response-related functional connectivity was detected in the visual cortex, cerebellum, brainstem, and MCC/PCC with the right anterior insula and its adjacent regions as seed regions. Thus, the right anterior insula and adjacent regions, in collaboration with other regions play a role in eliciting anxiety based on the prediction of negative events, by mediating anxiety-related autonomic responses according to interoceptive information.

neuroscience↗

bioRxiv2021

Transcriptional plasticity drives leukemia immune escape

Relapse of acute myeloid leukemia (AML) after allogeneic bone marrow transplantation (alloSCT) has been linked to immune evasion due to reduced expression of major histocompatibility complex class II (MHC-II) proteins through unknown mechanisms. We developed CORENODE, a computational algorithm for genome-wide transcription network decomposition, that identified the transcription factors (TFs) IRF8 and MEF2C as positive regulators and MYB and MEIS1 as negative regulators of MHC-II expression in AML cells. We show that reduced MHC-II expression at relapse is transcriptionally driven by combinatorial changes in the levels of these TFs, acting both independently and through the MHC-II coactivator CIITA. Beyond the MHC-II genes, MYB and IRF8 antagonistically regulate a broad genetic program responsible for cytokine signaling and T-cell stimulation that displays reduced expression at relapse. A small number of cells with altered TF levels and silenced MHC-II expression are present at the time of initial leukemia diagnosis, likely contributing to eventual relapse. Our findings reveal an adaptive transcriptional mechanism of AML evolution after allogenic transplantation whereby combinatorial fluctuations of TF levels under immune pressure result in selection of cells with a silenced T-cell stimulation program.

genomics↗

bioRxiv2021

A distinct core regulatory module enforces oncogene expression in KMT2A-rearranged leukemia

A small set of lineage-restricted transcription factors (TFs), termed core regulatory circuitry (CRC), control cell identity and malignant transformation. Here, we integrated gene dependency, chromatin architecture and TF perturbation datasets to characterize 31 core TFs in acute myeloid leukemia (AML). Contrary to a widely accepted model, we detected a modular CRC structure with hierarchically organized, partially redundant and only sparsely interconnected modules of core TFs controlling distinct genetic programs. Rapid TF degradation followed by measurement of genome-wide transcription rates revealed that core TFs directly regulate dramatically fewer genes than previously assumed. Leukemias carrying KMT2A (MLL) rearrangements depend on the IRF8/MEF2 axis to directly enforce expression of the key oncogenes MYC, HOXA9 and BCL2. Our datasets provide an evolving model of CRC organization in human cells, and a resource for further inquiries into and therapeutic targeting of aberrant transcriptional circuits in cancer.

genomics↗

bioRxiv2021

The peripheral T cell population is associated with pneumonia severity in cynomolgus monkeys experimentally infected with severe acute respiratory syndrome coronavirus 2

The coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a global pandemic that began in December 2019. Lymphopenia is a common feature in severe cases of COVID-19; however, the role of T cell responses during infection is unclear. Here, we inoculated six cynomolgus monkeys, divided into two groups according to the CD3+ T cell population in peripheral blood, with two clinical isolates of SARS-CoV-2: one of East Asian lineage and one of European lineage. After initial infection with the isolate of East Asian lineage, all three monkeys in the CD3+ low group showed clinical symptoms, including loss of appetite, lethargy, and transient severe anemia with/without short-term fever, within 14 days post-infection (p.i.). By contrast, all three monkeys in the CD3+ high group showed mild clinical symptoms such as mild fever and loss of appetite within 4 days p.i. and then recovered. After a second inoculation with the isolate of European lineage, three of four animals in both groups showed mild clinical symptoms but recovered quickly. Hematological, immunological, and serological tests suggested that the CD3+ high and low groups mounted different immune responses during the initial and second infection stages. In both groups, anti-viral and innate immune responses were activated during the early phase of infection and re-infection. However, in the CD3+ low group, inflammatory responses, such as increased production of monocytes and neutrophils, were stronger than those in the CD3+ high group, leading to more severe immunopathology and failure to eliminate the virus. Taken together, the data suggest that the peripheral T lymphocyte population is associated with pneumonia severity in cynomolgus monkeys experimentally infected with SARS-CoV-2. Author summarySARS-CoV-2 infection causes an illness with clinical manifestations that vary from asymptomatic or mild to severe; examples include severe pneumonia and acute respiratory distress syndrome. Lymphopenia, which is common in severe COVID-19 cases, is characterized by markedly reduced numbers of CD4+ T cells, CD8+ T cells, B cells, and natural killer cells. Here, we showed that cynomolgus monkeys selected according to the T cell populations in peripheral blood have different outcomes after experimental infection with SARS-CoV-2. These findings will increase our understanding of disease pathogenesis and may facilitate the development of animal models for vaccine evaluation.

pathology↗

bioRxiv2020

The role of replication clamp-loader protein HolC of Escherichia coli in overcoming replication /transcription conflicts

In Escherichia coli, DNA replication is catalyzed by an assembly of proteins, the DNA polymerase III holoenzyme. This complex includes the polymerase and proofreading subunits as well as the processivity clamp and clamp loader complex. The holC gene encodes an accessory protein (known as x) to the core clamp loader complex and is the only protein of the holoenzyme that binds to single-strand DNA binding protein, SSB. HolC is not essential for viability although mutants show growth impairment, genetic instability and sensitivity to DNA damaging agents. In this study, to elucidate the role of HolC in replication, we isolate spontaneous suppressor mutants in a holC{Delta} strain and identify these by whole genome sequencing. Some suppressors are alleles of RNA polymerase, suggesting that transcription is problematic for holC mutant strains or sspA, stringent starvation protein. Using a conditional holC plasmid, we examine factors affecting transcription elongation and termination for synergistic or suppressive effects on holC mutant phenotypes. Alleles of RpoA (), RpoB ({beta}) and RpoC ({beta}) RNA polymerase holoenzyme can partially suppress loss of HolC. In contrast, mutations in transcription factors DksA and NusA enhanced the inviability of holC mutants. Mfd had no effect nor did elongation factors GreA and GreB. HolC mutants showed enhanced sensitivity to bicyclomycin, a specific inhibitor of Rho-dependent termination. Bicyclomycin also reverses suppression of holC by rpoA rpoC and sspA.These results are consistent with the hypothesis that transcription complexes block replication in holC mutants and Rho-dependent transcriptional termination and DksA function are particularly important to sustain viability and chromosome integrity. IMPORTANCETranscription elongation complexes present an impediment to DNA replication. We provide evidence that one component of the replication clamp loader complex, HolC, of E. coli is required to overcome these blocks. This genetic study of transcription factor effects on holC growth defects implicates Rho-dependent transcriptional termination and DksA function as critical. It also implicates, for the first time, a role of SspA, stringent starvation protein, in avoidance or tolerance of replication/replication conflicts. We speculate that HolC helps resolve codirectional collisions between replication and transcription complexes, which become toxic in HolCs absence.

genetics↗

bioRxiv2020

Extending the integrate-and-fire model to account for metabolic dependencies

It is widely accepted that the brain, like any other physical system, is subjected to physical constraints restricting its operation. The brains metabolic demands are particularly critical for proper neuronal function, but the impact of these constraints is still poorly understood. Detailed single-neuron models are recently integrating metabolic constraints, but the computational resources these models need, make it difficult to explore the dynamics of extended neural networks imposed by such constraints. Thus, there is a need for a simple-enough neuron model that incorporates metabolic activity and allows us to explore neural network dynamics. This work introduces an energy-dependent leaky integrate-and-fire (LIF) neuronal model extension to account for the effects of metabolic constraints on the single-neuron behavior (EDLIF). This simple energy-dependent model shows better performance predicting real spikes trains -in spike coincidence measure sense-than the classical leaky integrate-and-fire model. It can describe the relationship between the average firing rate and the ATP cost, and replicate a neurons behavior under a clinical setting such as amyotrophic lateral sclerosis. The simplicity of the energy-dependent model presented here, makes it computationally efficient and thus, suitable to study the dynamics of large neural networks. Author summaryAny physical system or biological tissue is restricted by physical constraints bounding their behavior, and the brain is not free from these constraints. Energetic disorders in the brain have been linked to several neurodegenerative diseases, highlighting the relevance of maintaining a critical balance between energy production and consumption in neurons. These observations motivate the development of mathematical tools that can help to understand the dependence of the brains behavior in metabolism. One of the essential building blocks to achieve this task is the mathematical representation of neurons through models, allowing computational simulations of single-neurons and neural networks. Here we construct a simple and computational cheap energy-dependent neuron model that allows the study of neurons behavior under an energetic perspective. The introduced neuron model is contrasted with one of the widest-used neuron models and shows better prediction capabilities when real neuron recordings are used. Our model is suitable for replicating neurons behavior under a specific neurodegenerative disease, which cannot be achieved by the abovementioned popular model. Our simple model is promising because it allows the simulation and study of neuronal networks under a metabolic-dependent perspective.

neuroscience↗

bioRxiv2020

Culture influences audiovisual emotion perception in early sensory areas

Emotion perception from facial and vocal expressions is a multisensory process critical for human social interaction. When asked to judge emotions by attending to either face or voice, the accuracy was higher when facial expressions are congruent with vocal expressions than when they are incongruent. This congruency effect was shown to be affected by cultural background. Here we conducted functional MRI alongside a multisensory emotion perception task involving Japanese and Dutch participants. They were presented with movies in which congruent or incongruent emotions were expressed through faces and voices. The participants were asked to judge the emotion of either the face or the voice. Consistent with previous studies, behavioral results showed an interaction between group and task. fMRI results revealed that during voice-based judgement, congruency effects of the primary visual cortex, by means of the task related activity of congruent stimuli subtracted by that of incongruent stimuli, were more prominent in the Dutch group than in Japanese group. Finally, behavioral and neural congruency effects of the primary visual cortex were positively correlated only in the Dutch group. Taken together, our results show that culture affects the activities of early sensory areas in multisensory perception from facial and vocal expressions.

neuroscience↗

bioRxiv2018

Luigi: Large-scale histopathological image retrieval system using deep texture representations

BackgroundAs a large number of digital histopathological images have been accumulated, there is a growing demand of content-based image retrieval (CBIR) in pathology for educational, diagnostic, or research purposes. However, no CBIR systems in digital pathology are publicly available.\n\nResultsWe developed a web application, the Luigi system, which retrieves similar histopathological images from various cancer cases. Using deep texture representations computed with a pre-trained convolutional neural network as an image feature in conjunction with an approximate nearest neighbor search method, the Luigi system provides fast and accurate results for any type of tissue or cell without the need for further training. In addition, users can easily submit query images of an appropriate scale into the Luigi system and view the retrieved results using our smartphone application. The cases stored in the Luigi database are obtained from The Cancer Genome Atlas with rich clinical, pathological, and molecular information. We tested the Luigi system by querying typical cancerous regions from four cancer types, and confirmed successful retrieval of relevant images.\n\nConclusionsThe Luigi system will help students, pathologists, and researchers easily retrieve histopathological images of various cancers similar to those of the query image.

pathology↗