Biology subjects

Nomura, S.

Publications and source records attributed to Nomura, S..

18 recordsLinked to original sources

bioRxiv2026

A genome-wide catalog of sites where peripheral DNA methylation reflects the brain

Epigenetic studies of psychiatric and neurological disorders rely largely on peripheral tissues, yet where peripheral DNA methylation (DNAm) reflects the brain remains unclear. We generated a paired brain and peripheral DNAm dataset from 148 donors in three cohorts and combined it with five published cohorts for consensus brain-peripheral correlations. By cross-validation across cohorts, we defined brain epigenome shared sites (BrESS), more than 100,000 CpGs per tissue at which peripheral DNAm reproducibly predicts brain DNAm. BrESS lay at promoters active in both brain and periphery and in housekeeping genes, and most were not explained by genetic effects. BrESS did not contribute to the heritability of seven disorders, and CpGs from epigenome-wide association studies of these disorders were not enriched at BrESS. Peripheral DNAm reflects the brain mainly in a regulatory compartment shared across tissues, outside which disease signals largely lie, and BrESS separate peripheral signals attributable to the brain from others.

neuroscience↗

bioRxiv2026

SIK3 links synaptic strength to sleep pressure through RhoA signaling

Sleep is regulated by homeostatic sleep pressure, which accumulates during wakefulness, triggering sleep, and dissipates during sleep, leading to wakefulness. Although recent evidence suggests that synaptic potentiation encodes sleep pressure, the intracellular mechanisms linking synaptic strength to sleep pressure remain unclear. Here we demonstrate that the sleep-promoting kinase SIK3 links synaptic strength and sleep pressure through RhoA signalling. We found that SIK3 is required for dendritic spine enlargement induced by chemical long-term potentiation (cLTP) in cultured cortical pyramidal neurons and positively regulates spine size in the prefrontal cortex in vivo. cLTP reduced RhoA activity in an SIK3-dependent manner during spine enlargement, whereas activation of RhoA reduced EEG delta density in vivo during non-rapid eye movement sleep (NREMS), an indicator of sleep pressure. SIK3 substrate screening identified several RhoA regulators including GEF-H1, and further biochemical analyses found that phosphorylation by SIK3 activates GEF-H1. However, contrary to our expectation, RhoA facilitation through pharmacological activation of GEF-H1 enlarged spine size in cultured neurons, and expression of constitutively active GEF-H1 increased NREMS delta density in a RhoA-dependent fashion. Together, these results indicate that SIK3 enlarges spine size and enhances NREMS delta density through two RhoA-dependent pathways, driving mutually opposing intermediate phenotypes. Our findings identify two clashing SIK3-RhoA signalling pathways that couple synaptic regulation to sleep homeostasis.

neuroscience↗

bioRxiv2026

Tumor-Derived SPP1 Drives Immunosuppressive Macrophage Reprogramming in Gastric Peritoneal Carcinomatosis

Peritoneal carcinomatosis is a major cause of death in gastric cancer, yet effective therapies remain limited. Tumor-derived soluble factors are increasingly recognized as key regulators of the peritumoral microenvironment. Here, we nominate osteopontin (SPP1) as a tumor-derived mediator that orchestrates macrophage-driven immunoregulation in gastric peritoneal carcinomatosis. Using integrated analyses of human clinical datasets and murine models, we demonstrate that tumor-secreted SPP1 promotes macrophage recruitment and induces tolerogenic IL-10 production. Clinically, SPP1 correlated with inferior overall survival and progression-free survival in gastric cancer. In syngeneic murine models of gastric peritoneal carcinomatosis, intracavitary pharmacologic inhibition of SPP1 restricted peritoneal dissemination, impaired macrophage infiltration and suppressed IL-10 production. Consistent with these findings, macrophage depletion phenocopied antitumor effects of SPP1 inhibition, resulting in decreased metastatic burden. Collectively, these findings define a mechanism of tumor-macrophage crosstalk that promotes peritoneal dissemination and provide a rationale for therapeutic targeting of SPP1 in gastric peritoneal carcinomatosis.

Cancer Biology↗

bioRxiv2025

A gastric microbial chromatin remodeler drives gastric cancer progression and immune evasion by reprogramming the host epigenome

Emerging evidence highlights the crucial role of microbial communities in modulating cancer development and progression. In gastric cancer (GC), we identify Streptococcus anginosus (SA) as a tumor-resident oncobacterium that drives both tumor progression and immune evasion. We define a novel mechanism in which SA secretes extracellular vesicles (saEVs) that translocate the bacterial chromatin remodeler saSNF2 into host cell. There, saSNF2 partners with host transcription factor TEAD1--through its ATPase activity and participation in BAF complex assembly--to coordinately activate oncogenic transcription. This transkingdom interaction upregulates the palmitoyltransferase ZDHHC11, which in turn stabilizes PD-L1 via palmitoylation to establish an immunosuppressive niche, while also amplifying other TEAD1 target genes to fuel tumor progression. Functionally, saEVs promote tumor growth and limit CD8+ T-cell infiltration in vivo. Strikingly, pharmacological inhibition of ZDHHC11 reverses immune evasion and synergizes with anti-PD-1 checkpoint blockade. Our results establish SA as a multifaceted driver of GC and reveal the saSNF2-ZDHHC11 axis as a promising target to potentiate immunotherapy.

cancer biology↗

bioRxiv2025

Hox - Meis-relayed topographical genetic switch underlies cardiopharyngeal neural crest diversification, revealed by multimodal analysis

Neural crest cells (NCCs) are multipotent migratory cells essential for cardiac development, yet the lineage trajectories and gene regulatory networks (GRNs) underlying their differentiation in the cardiopharyngeal region remain unclear. Here, we integrate single-cell RNA-seq, spatial transcriptomics, and multiomic analyses to construct a comprehensive map of NCC lineages in developing mouse cardiopharyngeal tissues. We identify a transition from Hox-positive pharyngeal NCCs to Hox-negative intracardiac populations associated with the outflow tract cushion, accompanied by a shift in Meis transcription factor binding and GRN architecture. By contrast, NCCs forming the aorticopulmonary septum and great vessel smooth muscle retain distinct Hox-codes. A Meis2-Sox9-Scx GRN defines a skeletogenic progenitor-like intermediate state that gives rise to coronary artery smooth muscle and semilunar valves. Our findings suggest that the loss of Hox-dependent regional identity enables pharyngeal NCCs to acquire new fates upon entering the cardiac cushion, providing insight into the developmental origins of coronary and valvular calcification.

developmental biology↗

bioRxiv2025

Novel therapy for gastric cancer peritoneal dissemination using genetically modified dental pulp cells and astatine-211

Peritoneal dissemination of gastric cancer is a terminal stage with limited treatment options and a five-year survival rate below 10%. To develop a more effective treatment, we created a new approach that uses genetically engineered human dental pulp cells (DPCs) that express the sodium/iodide symporter (NIS). These cells (NIS-DPCs) deliver astatine-211 (At-211) directly to tumor sites. When injected intraperitoneally into a mouse model of gastric cancer dissemination, DPCs, which were isolated and expanded, showed strong tumor-homing ability. Chemotaxis mediated by the CXCR4/SDF-1 axis has been reported to play a role in this accumulation. In addition to histological analysis, fluorescent imaging confirmed the selective accumulation of NIS-DPCs within tumor lesions. Introducing the NIS gene markedly increased SLC5A5 expression, enabling efficient At-211 uptake. To avoid nonspecific binding, sodium At-211 was utilized. High-resolution alpha-particle imaging visualized alpha-ray emission specifically from NIS-DPCs, confirming the radionuclides intracellular retention. In vivo, the sequential administration of NIS-DPCs, followed by Na[At-211], resulted in the pronounced regression of peritoneal tumors and a significant extension of survival compared to controls. The therapeutic mechanism involves three coordinated steps: tumor-directed migration of NIS-DPCs, At-211 uptake via NIS transporters, and localized alpha-particle-mediated cytotoxicity. This study introduces the novel concept of cell-based alpha-radiotherapy, which integrates regenerative and nuclear medicine. Due to the well-documented safety profile of DPCs in human clinical trials (J-REPAIR, jRCT1080224505), the NIS-DPC platform emerges as a promising approach for the precise, localized irradiation of disseminated gastric cancer and other challenging malignancies.

cancer biology↗

bioRxiv2025

Bioengineered iPSC Vessels Recapitulate Human Vascular Physiological Function and Aging Phenotypes

Vascular aging contributes to multisystem diseases and limits health span. Although various animal models have contributed to aging research, their vasculatures poorly recapitulate human physiology. Even existing tissue-engineered blood vessels fail to mimic human vascular function and pathology, hindering translational advances in vascular aging studies. Here, we present a novel human physiological vascular model fabricated via the unique molding-induced circumferential alignment of human induced pluripotent stem cell (iPSC)-derived vascular smooth muscle cells with luminally seeded endothelial cells. This architecture enabled dynamic vasodiameter changes in response to vasoactive stimuli, including hormones and intraluminal pressure. Using iPSCs from a patient with Werner syndrome, the model recapitulated aging-associated phenotypes, such as hypercontractility and increased vascular compliance, possibly due to impaired nitric oxide bioavailability. Transcriptomic and metabolomic analyses revealed age-related dysregulation consistent with vascular senescence. As a key advantage of the vasculature, spatial transcriptomic analysis demonstrated upregulation of the aging marker CDKN1A near the lumen and downregulation of COL6A1 and TPM1 throughout the vessel. Treatment with mitochonic acid 5, a mitochondria-targeted compound, significantly reversed the aging phenotypes. These findings demonstrate that our engineered vascular model recapitulates key aspects of human vascular properties and provides a platform for mechanistic studies of vascular aging and drug discovery aimed at extending health span.

bioengineering↗

bioRxiv2025

DNA Specimen Preservation using DESS and DNA Extraction in Museum Collections: A Case Study Report

Recent advances in DNA research have increased the necessity for museums to preserve not only morphological specimens but also their DNA, leading us to maintain tissue samples linked to specimens at -80{degrees}C. DNA analysis has become an essential tool for taxonomic research and biodiversity assessment; however, freezer storage for all samples is impractical due to space limitations and operational costs. This creates a pressing need to develop more widely applicable DNA preservation methods. We investigated the comparative effects of traditional preservation methods versus DESS (DMSO/EDTA/saturated NaCl solution) preservation on both morphology and DNA integrity using museum specimens from various taxonomic groups. Our results demonstrated that DESS preservation maintained high-quality DNA fragments exceeding >15 kb at room temperature across all examined species, with nematode samples maintaining DNA integrity even after 10 years of storage. When preserving whole organisms, the optimal preservation solution conditions for maintaining both morphological features and DNA integrity varied among species. Notably, DNA integrity was maintained even after complete evaporation of the DESS solution. These findings suggest that DESS utilization for specimen DNA preservation is effective across many species, not only for long-term storage in environments without freezer facilities but also for temporary preservation until freezing. Simple SummaryRecent advances in DNA research have increased the necessity for museums to preserve not only morphological specimens but also their DNA, leading us to maintain tissue samples linked to specimens at -80{degrees}C. However, as freezer storage for all samples is impractical, there is a pressing need to develop more widely applicable DNA preservation methods. In this study, we investigated the effectiveness of traditional preservation methods versus DESS (DMSO/EDTA/saturated NaCl solution) preservation with regards to both morphology and DNA integrity using our museum specimens. Our results demonstrated that DESS preservation maintained high molecular weight DNA at room temperature across all examined species. When preserving whole organisms, the optimal preservation solution conditions for maintaining both morphological features and DNA integrity varied among species. Notably, DNA integrity was maintained even after complete evaporation of the DESS solution. These findings suggest that DESS utilization for specimen DNA preservation is effective across many species, not only for long-term storage in environments without freezer facilities but also for temporary preservation until freezing is possible.

zoology↗

bioRxiv2024

mmVelo: A deep generative model for estimating cell state-dependent dynamics across multiple modalities

Single-cell multiomics provides unique insight into the regulatory relationships across different biological layers such as the transcriptome and regulome. However, single-cell multiomics is limited by its ability to capture only static snapshots at the time of observation, restricting the reflection of dynamic state changes orchestrated across modalities. RNA velocity analysis of single cells allows for the prediction of temporal changes in the transcriptome; however, the inferred dynamics cannot be applied across all biological layers, specifically in the regulome. Therefore, to address this limitation, we developed multimodal velocity of single cells (mmVelo), a deep generative model designed to estimate cell state-dependent dynamics across multiple modalities. mmVelo estimates cell state dynamics based on spliced and unspliced mRNA expression, and uses multimodal representation learning to project these dynamics onto chromatin accessibility, inferring chromatin velocity at a single-peak resolution. We applied mmVelo to single-cell multiomics data from a developing mouse brain and validated the accuracy of the estimated chromatin accessibility dynamics. Furthermore, using the estimated dynamics, we identified the transcription factors that are crucial for chromatin accessibility regulation in mouse skin. Finally, using multiomics data as a bridge, we demonstrated that during human brain development, the dynamics of missing modalities can be inferred from single-modal data via cross-modal generation. Overall, mmVelo enhances our understanding of the dynamic interactions between modalities, offering insights into the regulatory relationships across molecular layers.

bioinformatics↗

bioRxiv2024

A deep generative model integrating single-cell time-frequency characteristics transformed from electrophysiological data with transcriptomic features

Patch-seq yields multi-modal data (e.g., transcriptomic and electrophysiological data) from single cells. However, currently used analytical methods are based on a few global electrophysiological features predefined from chronological potential changes and overlook the importance of time-frequency domain. In this study, we present LincSpectr, a deep neural network model that integrates transcriptomic and electrophysiological features with the latent variables of various variational autoencoders. This model combines the two modalities according to the connection between the latent variables of different modalities calculated by attention-like mechanisms and achieves cross-modal predictions and an inverse analysis. We discovered that the predicted electrophysiological features changed continuously along with their transcriptional profiles and that the neighborhood relationships between the latent states of the transcriptional profiles were consistent with those of the electrophysiological features. Inverse analysis of our model enabled the extraction of gene sets affecting specific time-frequency domains; some genes were likely to be involved in neural activity. Our approach represents a potential avenue to facilitate the discovery of molecular mechanisms underlying time-frequency activities in various cell types, enhancing our understanding of their roles in neural function.

bioinformatics↗

bioRxiv2024

ARViS: A bleed-free multi-site automated injection robot for accurate, fast, and dense delivery of virus to mouse and marmoset brains

Genetically encoded fluorescent sensors continue to be developed and improved. If they could be expressed across multiple cortical areas in non-human primates, it would be possible to measure a variety of spatiotemporal dynamics of primate-specific cortical activity. Here, we develop an Automated Robotic Virus injection System (ARViS) for broad expression of a biosensor. ARViS consists of two technologies: image recognition of vasculature structures on the cortical surface to determine multiple injection sites without hitting them, and robotic control of micropipette insertion perpendicular to the cortical surface with 50-m precision. In mouse cortex, ARViS sequentially injected virus solution into 100 sites over a duration of 100-minutes with a bleeding probability of only 0.1% per site. Furthermore, ARViS successfully achieved 266-site injections over the frontoparietal cortex of a common marmoset. We demonstrate one-photon and two-photon calcium imaging in the marmoset frontoparietal cortex, illustrating the effective expression of biosensors delivered by ARViS.

neuroscience↗

bioRxiv2023

A deep generative model for estimating single-cell RNA splicing and degradation rates

AO_SCPLOWBSTRACTC_SCPLOWMessenger RNA splicing and degradation are critical for gene expression regulation, the abnormality of which leads to diseases. Previous methods for estimating kinetic rates have limitations, assuming uniform rates across cells. We introduce DeepKINET, a deep generative model that estimates splicing and degradation rates at single-cell resolution from scRNA-seq data. DeepKINET outperformed existing methods on simulated and metabolic labeling datasets. Applied to forebrain and breast cancer data, it identified RNA-binding proteins responsible for kinetic rate diversity. DeepKINET also analyzed the effects of splicing factor mutations on target genes in erythroid lineage cells. DeepKINET effectively reveals cellular heterogeneity in post-transcriptional regulation.

bioinformatics↗

bioRxiv2022

Inflammatory response induced in pulmonary embolic lung: Evaluation usinga reproducible murine pulmonary embolism model.

BackgroundSince previously established models of pulmonary embolism showed a large variability in the degree of ischemia, it is difficult to assess the pathophysiological response in the lung after embolization. Here, we established a model of pulmonary embolism by certain amount of relatively small thrombi, in which the degree of ischemia was reproducible. MethodsThrombi with a maximum diameter of 100 m or 500 m were administered intravenously under anesthesia, and the survival ratio at 4 hours was evaluated. The location of thrombi in the lung was visualized by administration of fluorescent-labeled thrombus, and the hemodynamics of the lung after administration of thrombi was evaluated. CT angiography was also performed to evaluate the ratio of the embolized vessels. In addition, cytokine mRNAs was quantified 4 hours in embolized lung. Immunohistochemical analysis for interleukin (IL)-6 and CD68 as a marker of macrophages were also performed. ResultsIt was found that mice with 100 m clots, but not with 500 m clots, showed a dose-dependence of survival between 2.3 L/g and 3.0 L/g at 4 hours from embolization induction. In mice treated with 2.5 L/g of 100 m thrombus, thrombi were located in the peripheral region of the lung, which was consistent with the disruption of blood circulation the peripheral region. In addition, about 60% of the vessels with a diameter of less than 100 m were occluded in these mice. In the lungs after 4 hours of embolization, IL-6 mRNA and tumor necrosis factor (TNF)- mRNA were significantly higher and lower than control lungs. IL-6 was expressed in CD68-positive macrophages in both embolized and control lungs after 4 hours of embolization, and the number of each positive cells were comparable in both embolized and control lungs. ConclusionsThese results show that the pulmonary embolization model induced by a certain amount of small thrombus is useful for evaluating the pathological responses in the embolized lung. Furthermore, it was found that IL-6 expression was increased in macrophages in the embolized lung, indicating that inflammatory responses may contribute to the pathogenesis of pulmonary embolism.

pathology↗

bioRxiv2022

Cardiac neural crest lineage diversity and underlying gene regulatory networks revealed by multimodal analysis

Neural crest cells (NCCs), a multipotent stem cell population, contribute to cardiac development as a source of the outflow septum, vascular smooth muscle and semilunar valves. However, genetic programs underlying lineage diversification of cardiac NCCs remain largely unknown. Using single-cell (sc) and spatial transcriptomics, we demonstrate multiple NCC subpopulations with distinct gene expression signatures; smooth muscle(-like), non-muscle mesenchymal, and Schwann cell progenitor/melanoblast-like cells. Integrative scRNA-seq and scATAC-seq analyses predict lineage trajectories starting from immature NCCs, which bifurcate into smooth muscle(-like) and non-muscle mesenchymal lineages in association with hierarchical transcription factor networks. Combinatory analyses with Cre-mediated genetic lineage tracing characterize intermediate NCCs at the bifurcation as Sox9+/Scx+ tendon and cartilage progenitor-like cells with genetic programs, some of which are common to skeletal tissues whereas others are unique to cardiac NCCs. These findings provide a basis for understanding the roles of NCCs in cardiac development and pathogenesis particularly associated with calcification.

developmental biology↗

bioRxiv2021

Software for Non-Parametric Image Registration of 2-Photon Imaging Data

Functional 2-photon microscopy is a key technology for imaging neuronal activity. The recorded image sequences, however, can contain non-rigid movement artifacts which requires high-accuracy movement correction. Variational optical flow (OF) estimation is a group of methods for motion analysis with established performance in many computer vision areas. However, it has yet to be adapted to the statistics of 2-photon neuroimaging data. In this work, we present the motion compensation method Flow-Registration that outperforms previous alignment tools and allows to align and reconstruct even low signal-to-noise ratio 2-photon imaging data and is able to compensate high-divergence displacements during local drug injections. The method is based on statistics of such data and integrates previous advances in variational OF estimation. Our method is available as an easy-to-use ImageJ / FIJI plugin as well as a MATLAB toolbox with modular, object oriented file IO, native multi-channel support and compatibility with existing 2-photon imaging suites.

neuroscience↗

bioRxiv2019

Population-specific and transethnic genome-wide analyses reveal distinct and shared genetic risks of coronary artery disease

To elucidate the genetics of coronary artery disease (CAD) in the Japanese population, we conducted a large-scale genome-wide association study (GWAS) of 168,228 Japanese (25,892 cases and 142,336 controls) with genotype imputation using a newly developed reference panel of Japanese haplotypes including 1,782 CAD cases and 3,148 controls. We detected 9 novel disease-susceptibility loci and Japanese-specific rare variants contributing to disease severity and increased cardiovascular mortality. We then conducted a transethnic meta-analysis and discovered 37 additional novel loci. Using the result of the meta-analysis, we derived a polygenic risk score (PRS) for CAD, which outperformed those derived from either Japanese or European GWAS. The PRS prioritized risk factors among various clinical parameters and segregated individuals with increased risk of long-term cardiovascular mortality. Our data improves clinical characterization of CAD genetics and suggests the utility of transethnic meta-analysis for PRS derivation in non-European populations.

genetics↗

bioRxiv2019

Transethnic meta-analysis of genome-wide association studies identifies three new loci and characterizes population-specific differences for coronary artery disease

BackgroundGenome-wide association studies (GWAS) provided many biological insights into coronary artery disease (CAD), but these studies were mainly performed in Europeans. GWAS in diverse populations have the potential to advance our understanding of CAD.\n\nMethods and ResultsWe conducted two GWAS for CAD in the Japanese population, which included 12,494 cases and 28,879 controls, and 2,808 cases and 7,261 controls, respectively. Then, we performed transethnic meta-analysis using the results of the CARDIoGRAMplusC4D 1000 Genomes meta-analysis with UK Biobank. We identified 3 new loci on chromosome 1q21 (CTSS), 10q26 (WDR11-FGFR2), and 11q22 (RDX-FDX1). Quantitative trait locus analyses suggested the association of CTSS and RDX-FDX1 with atherosclerotic immune cells. Tissue/cell type enrichment analysis showed the involvement of arteries, adrenal glands and fat tissues in the development of CAD. Finally, we performed tissue/cell type enrichment analysis using East Asian-frequent and European-frequent variants according to the risk allele frequencies, and identified significant enrichment of adrenal glands in the East Asian-frequent group while the enrichment of arteries and fat tissues was found in the European-frequent group. These findings indicate biological differences in CAD susceptibility between Japanese and Europeans.\n\nConclusionsWe identified 3 new loci for CAD and highlighted the genetic differences between the Japanese and European populations. Moreover, our transethnic analyses showed both shared and unique genetic architectures between the Japanese and Europeans. While most of the underlying genetic bases for CAD are shared, further analyses in diverse populations will be needed to elucidate variations fully.

genetics↗

bioRxiv2019

Highly reliable, targeted photothermal cancer therapy combined with thermal dosimetry using indocyanine green lactosome

Indocyanine green (ICG) is a near-infrared light-absorbing substance. Thus, when a tumor in which ICG has accumulated is irradiated with a near-infrared (NIR) laser, only the tumor can be heated by a photothermal reaction. We developed ICG lactosome, a novel drug delivery system (DDS) composed of polymeric micelles and ICG that shows selective accumulation in tumor based on an enhanced permeability and retention (EPR) effect. We showed that ICG lactosome accumulated in a tumor by using an intradermal tumor mouse model of a murine colon cancer cell line (Colon26) transfected with Nano lantern luminescent protein (NLC26). Two days after the administration of ICG lactosome, the tumor was irradiated with an 808-nm diode-laser while monitoring tumor temperature. The results showed that the treated tumors were cured when the peak of tumor temperature during NIR irradiation reached 43{degrees}C or higher. To verify these results, photothermal therapy (PTT) using ICG lactosome was carried out using a newly developed system that can control the temperature at the NIR irradiation site at a constant level. All of the tumors that had been kept at 43{degrees}C during irradiation were cured, while 2 of 5 tumors that had been kept at 42{degrees}C were not cured, and none of tumors that had been kept at a temperature below 41{degrees}C were cured. ICG lactosome-assisted PTT combined with thermal dosimetry is a highly reliable method for cancer treatment and may afford further clinical opportunities for PTT.

bioengineering↗