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Hattori, K.

Publications and source records attributed to Hattori, K..

At least 19 recordsLinked to original sources

Large-scale dimensional behavioral profiling dissociates fear memory from locomotor confounds in mice: The necessity of baseline-normalized metrics

Fear conditioning is widely used to assess associative memory in mice, yet percent freezing conflates memory with baseline locomotor and anxiety-related traits. A systematic survey of recent studies (2020-2025) found that fewer than 1% statistically integrate locomotor activity into freezing analyses. Here, we address this gap using a large-scale dataset of >10,000 mice across >160 comparisons, including genetic mutations, pharmacological interventions and aging, tested in 15 standardized behavioral paradigms. Conventional freezing scores covaried strongly with general locomotor activity, obscuring memory-related phenotypes. Multiple factor analysis identified two principal behavioral dimensions, locomotor activity and learning/memory: conventional freezing aligned with the locomotor dimension, whereas freezing subtraction and the activity suppression ratio mapped onto the memory dimension and improved detection of synaptic plasticity phenotypes. These analyses show that baseline locomotor normalization is essential for interpreting fear conditioning as a memory assay and provide an open framework for selecting and reporting locomotor-normalized metrics.

neuroscience↗

Organoid-in-Bead (OrB): vortex-based compartmentalization enables scalable, high-density intestinal organoid culture

Intestinal organoids are powerful in vitro models, but their use in large-scale analyses remains constrained by the low throughput, labor-intensive handling, and high reagent consumption of conventional Matrigel dome culture. Here, we present Organoid-in-Bead (OrB), a vortex-based compartmentalization workflow that partitions organoid fragments into thousands of discrete Matrigel microbeads, enabling scalable, high-density culture from a single batch preparation. OrB maintains dome-comparable organoid growth and epithelial polarity, supports passaging-based culture expansion, yields more than 5,000 organoids in the final 10 cm dish format, and reduces Matrigel and medium consumption by approximately 70% on a per-organoid basis. OrB therefore provides a practical and scalable upstream workflow for generating screening-scale intestinal organoids. HighlightsO_LIOrB generates Matrigel microcompartments by vortexing without microfluidics C_LIO_LIOrB enables scalable, high-density intestinal organoid culture in one batch C_LIO_LIOrB maintains dome-comparable growth and epithelial polarity and supports passaging C_LIO_LIOrB yields >5,000 organoids per batch with [~]70% less Matrigel/medium per organoid C_LI

bioengineering↗

Microfluidic Core-Shell Encapsulation Enables Scalable Generation of Apical-Out Intestinal Spheroids

Apical-out intestinal spheroids provide direct access to the lumen-facing epithelial surface, making them attractive three-dimensional models for studying epithelial barrier function, nutrient uptake, and luminal exposure. However, existing polarity-reversal methods typically require releasing spheroids from surrounding ECM gels and culturing them in suspension, which can compromise matrix-derived cues, promote fusion, increase size heterogeneity, and limit scalability. Here, we develop a microfluidic core-shell encapsulation strategy to scalably produce apical-out intestinal spheroids within uniform hydrogel microcapsules. These microcapsules consist of a Matrigel core surrounded by an agarose shell. Flow-focusing microfluidics first confines Caco-2 cells in Matrigel cores that provide instructive extracellular matrix cues, and particle-templated emulsification subsequently encloses each core within an inert agarose shell that prevents spheroid fusion and preserves batch uniformity. The method generated >100,000 microcapsules per experiment, with a mean shell diameter of 117 {micro}m, a coefficient of variation below 9%, and >90% single-spheroid formation efficiency. The resulting spheroids established apical-basolateral polarity, organised tight junctions, formed a dextran-excluding epithelial barrier, and exhibited fatty-acid uptake. This core-shell strategy provides an experimentally tractable platform for scalable intestinal epithelial modelling and may be extensible to other epithelial microtissue systems. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=42 SRC="FIGDIR/small/731294v2_ufig1.gif" ALT="Figure 1"> View larger version (16K): org.highwire.dtl.DTLVardef@16dc3forg.highwire.dtl.DTLVardef@d5d947org.highwire.dtl.DTLVardef@1abe79forg.highwire.dtl.DTLVardef@f39239_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

Collagen Rope Trick: Cell-Laden Fibre Assembly at 1 Liquid Interfaces

Summary ParagraphTissues and organs in living organisms represent centimeter-scale hierarchical architectures comprising nano-to microscale, uniaxially aligned extracellular matrix (ECM) fibres with high mechanical strength, integrated with cellular components, as exemplified in tendon, skin, cartilage, bone, and blood vessels1. Here, we present a liquid-liquid interfacial spinning method to produce highly uniaxially aligned, centimeter-scale collagen fibres. The dried fibres exhibit exceptional mechanical properties, with fracture strength of 280 MPa, Youngs modulus of 6 GPa, and toughness of 17 MJ m-3, comparable to spider silk and tendon collagen, and exceeding supramolecular and double-network hydrogels1. Incorporating living cells into the collagen solution yielded centimeter-scale, cell-laden aligned fibres, with densely adherent, uniaxially aligned cells and over 80% viability. Myoblast-laden fibres recapitulate biological features of fibrotic muscle tissues, as observed in type II diabetes2. Interfacial collagen assembly further enables fabrication of dimension-controlled constructs, like 2D sheets, 0D capsules, and 1D tubes, thus providing modular building blocks for centimeter-scale 3D tissues and organ-like structures. This approach offers a versatile platform to engineer mechanically robust, cell-laden tissues with controlled hierarchical architecture.

bioengineering↗

eeeHive: a new HF RFID-based automated behavioral monitoring system for group-housed animals with high spatiotemporal resolution

Long-term, automated tracking of group-housed social animals using RFID (radio frequency identification) is a promising approach in ethological neuroscience. However, low-frequency (LF) RFID, while long-established in the field, is constrained by its inherent low data rates, which lead to two critical limitations: (1) compromised spatiotemporal resolution, and (2) the inability to identify multiple tags (animals) simultaneously. To address these limitations, we developed eeeHive, a high-frequency (HF) RFID-based animal tracking system with a fully custom hardware architecture that enables high-speed, multiplexed antenna polling and concurrent multi-tag reading. The polling time per antenna in eeeHive was 5.9 ms, with an additional 8.2 ms read time per tag. We applied the system to track 24 mice for one week, and six common marmosets for seven weeks. The system successfully tracked individuals even within dense clusters, revealing complex behavioral traits characterized by spatial utilization, temporal dynamics, behavioral regularity, and inter-individual relationships. Additional tests with Japanese fire-bellied newts and Nile tilapia juveniles demonstrated comparable tracking performance in aquatic environments. Taken together, eeeHive overcomes the inherent limitations of conventional LF RFID, establishing a powerful HF RFID-based platform for fine-scale behavioral tracking of group-housed animals across terrestrial and aquatic species.

animal behavior and cognition↗

Tsunahiki task: A newly developed group-based operant task for mice

A group of social animals, including humans, distributes work and rewards and establishes inter-individual relationships through shared experiences of working together. Understanding the neural mechanisms underlying group work is essential for elucidating how social relationships are formed. Thus, a behavioral paradigm for studying group work in laboratory rodents is required. Here, we developed a Tsunahiki task, a novel group-based operant task for mice. In this task, three mice jointly pulled three ropes, and once all ropes were pulled out, all members gained access to a reward area, regardless of who performed the work. The mice acquired the task within a few days. Importantly, repeated experience with the Tsunahiki task led to a shift in workload toward subordinate individuals and induced rank consolidation. These findings suggest that group work induces consolidation of intra-group disparities based on the dominance hierarchy. The Tsunahiki task provides a useful framework for investigating the neurobiological mechanisms underlying collaborative work, group formation, and social inequality in rodents. TeaserA group-based operant task for mice was newly developed, in which hierarchy affected work and reward distributions.

animal behavior and cognition↗

Space-efficient method for high-throughput generation of uniform cell-laden hollow agarose microcapsules

Hollow hydrogel microcapsules isolate cells while allowing diffusion of nutrients and factors, supporting applications from single-cell analysis and clonal expansion to spheroid formation inside them. Conventional encapsulation relies on bulky instruments such as pumps and pressure controllers, hindering use in confined environments such as anaerobic chambers. Here we present a space-efficient method combining pump-free, -20 kPa negative-pressure droplet generation with particle-templated emulsification to produce millions of [~]70 {micro}m hollow agarose microcapsules using only a sealed bottle and a vortex mixer within a 30 cm x 30 cm footprint. The system maintains [~]491 {+/-} 2 drops/s and yields (2.26 {+/-} 0.09) x 106 capsules per batch with CV < 4% (N = 3). Operating entirely inside an anaerobic chamber, we encapsulated mouse gut bacteria and quantified population-level proliferation over four days. This space-efficient workflow enables high-throughput encapsulation under spatial constraints such as biosafety cabinets or anaerobic chambers, providing a practical foundation for downstream single-cell and clonal analyses.

bioengineering↗

Dietary soy shapes murine microbiota to consolidate the mucosal IgA response through T follicular helper cells

The commensal microbiota plays a crucial role in shaping mucosal immunity, particularly in the induction of T follicular helper (Tfh) cells and IgA production. Here, we demonstrate that dietary soy elicits a robust Tfh cell and IgA response in Peyers patches of weaning mice. Soy feeding promotes the expansion of two principal commensal bacterial species, Limosilactobacillus reuteri and Muribaculum intestinale. Mechanistically, L. reuteri provides cognate antigens for Tfh cell activation, while M. intestinale functions as an adjuvant by promoting IL-1{beta} production from myeloid cells. The resulting IgA exhibits polyreactivity and enhances protection against Salmonella infection. These findings highlight the specific interplay among dietary components, intestinal microbiota, and mucosal immunity, thereby establishing a diet-microbe-immune axis that shapes host defense in early life. This axis represents a promising therapeutic target for developing novel strategies to enhance resistance to enteric pathogens. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=170 HEIGHT=200 SRC="FIGDIR/small/669459v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@1ae8277org.highwire.dtl.DTLVardef@1f787ceorg.highwire.dtl.DTLVardef@1f51fd6org.highwire.dtl.DTLVardef@1fd3439_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIDietary soy promotes T follicular helper (Tfh) cell and IgA responses in the Peyers patches of weaning mice. C_LIO_LISoy enhances the colonization of two key commensals, Limosilactobacillus reuteri and Muribaculum intestinale, in the small intestine. C_LIO_LIThese two bacteria synergize to drive mucosal immunity: L. reuteri provides cognate antigens, while M. intestinale provides an adjuvant signal by promoting IL-1{beta} production from myeloid cells. C_LIO_LISoy-induced IgA is polyreactive and protects against Salmonella infection. C_LI

immunology↗

Efficient identification of antimalarials with novel mechanism of action via multi-sample transcriptomic profiling

Malaria poses a significant health burden to endemic countries, necessitating the development of new antimalarials with novel mechanisms of action to combat emerging drug resistance. However, target identification methods for antimalarial compounds selected through phenotypic screening are currently limited, which has been a major obstacle in the field of antimalarial drug discovery. Here, we aim to address this need using perturbation transcriptomics to efficiently select antimalarial compounds targeting new pathways or molecules. The method involves comparing the transcriptomic changes by drug perturbation in the asexual blood stage of the malaria parasite Plasmodium falciparum. Using this method, we identified several compounds that exhibited distinct transcriptomic profiling from a diverse set of antimalarials with known modes of action, indicating their potential to target different pathways. In addition, we successfully identified a novel histone deacetylase inhibitor using this approach and chemogenetically validated its target through in vitro evolution. These results highlight the effectiveness of this platform in accelerating antimalarial drug discovery.

microbiology↗

Large-scale generation of uniform sub-100 μm adipocyte spheroids in hydrogel microcapsules using a flow-focusing microfluidic device

Adipocyte spheroids are a promising three-dimensional (3D) cell culture model for obesity research because they reproduce 3D adipose tissue structures and cell-cell interactions better than 2D cultures. However, current methods fail to produce uniformly sized, small adipocyte spheroids at large scales, significantly limiting their use in analysis such as large-scale drug screening. Here, we develop a scalable method that combines simple microfluidics with templated emulsification to generate small, uniformly sized adipocyte spheroids. By encapsulating preadipocytes in numerous hollow agarose microcapsules and incubating them for two days, we reproducibly produced more than 100,000 uniform spheroids with diameters of approximately 50 {micro}m (CV: <13%); we then differentiated preadipocyte spheroids into adipocyte spheroids after an 8-day induction period. Our platform enhances large-scale 3D analysis using adipocyte spheroids for obesity research and can be adapted to generate various spheroid and organoid models, advancing biomedical research across diverse fields.

bioengineering↗

Heart generation via blastocyst complementation in Mesp1/2-deficient mice

Heart transplantation is the only curative option available for patients with advanced heart failure. However, donor organ shortage and graft rejection remain critical challenges in heart transplantation. Blastocyst complementation using pluripotent stem cells (PSCs) can be used to generate organs such as the pancreas and kidneys in animal models with abnormalities in essential developmental genes. Nonetheless, whether functional adult hearts can be generated with blastocyst complementation remains unclear, and it is unknown if parenchyma, blood vessels, and stroma can be generated concomitantly from PSCs using blastocyst complementation to avoid graft rejection. Here, we show the generation of functional adult hearts in acardiac Mesp1 and Mesp2 double-knockout (Mesp1/2-DKO) mice via blastocyst complementation using mouse PSCs. Our result shows that the generated hearts were structurally and functionally normal and restored embryonic lethality in Mesp1/2-DKO mice. All four cardiovascular lineages, including cardiomyocytes, vascular endothelial cells, smooth muscle cells, and cardiac fibroblasts, were virtually entirely derived from exogenous PSCs in the myocardium. Exogenous rat PSCs also generated rat-derived xenogeneic hearts in Mesp1/2-DKO mice via interspecies blastocyst complementation. Thus, blastocyst complementation is a viable technique for generating hearts derived from PSCs and may represent significant progress toward generating rejection-free hearts.

cell biology↗

Barcoding of small extracellular vesicles with CRISPR-gRNA enables comprehensive, subpopulation-specific analysis of their biogenesis/release regulators

Small extracellular vesicles (sEVs) are important intercellular information transmitters in various biological contexts, but their release processes remain poorly understood. Herein, we describe a high-throughput assay platform, CRISPR-assisted individually barcoded sEV-based release regulator (CIBER) screening, for identifying key players in sEV release. CIBER screening employs sEVs barcoded with CRISPR-gRNA through the interaction of gRNA and dead Cas9 fused with an sEV marker. Barcode quantification enables the estimation of the sEV amount released from each cell in a massively parallel manner. Barcoding sEVs with different sEV markers in a CRISPR pooled-screening format allows genome-wide exploration of sEV release regulators in a subpopulation-specific manner, successfully identifying previously unknown sEV release regulators and uncovering the exosomal/ectosomal nature of CD63+/CD9+ sEVs, respectively, as well as the synchronization of CD9+ sEV release with the cell cycle. CIBER should be a valuable tool for detailed studies on the biogenesis, release, and heterogeneity of sEVs.

cell biology↗

High-throughput 3D imaging flow cytometry of adherent 3D cell cultures

Three-dimensional (3D) cell cultures are indispensable in recapitulating in vivo environments. Among many 3D culture methods, the strategy to culture adherent cells on hydrogel beads to form spheroid-like structures is powerful for maintaining high cell viability and functions through an efficient supply of nutrients and oxygen. However, high-throughput, scalable technologies for 3D imaging of individual cells cultured on the hydrogel scaffolds are lacking. This study reports the development of a high-throughput, scalable 3D imaging flow cytometry (3D-iFCM) platform for analyzing spheroid models on hydrogel beads. This platform is realized by integrating a single objective lens-based fluorescence light-sheet microscopy with a microfluidic device employing a combination of hydrodynamic and acoustofluidic focusing techniques. This integration enabled an unprecedentedly high-throughput, robust optofluidic 3D imaging, processing 513 cells s-1 and a total of more than 104 cells within a minute. The large dataset obtained allows us to quantify and compare the nuclear morphology of adhering and suspended cells, revealing adhering cells have smaller nuclei with non-round surfaces. This platforms high throughput, robustness, and precision for analyzing the morphology of subcellular compartments in 3D culture models holds promising potential for various biomedical analyses, including image-based phenotypic screening of drugs with spheroids or organoids.

bioengineering↗

Analysis of histone H3K4me3 modifications in bovine placenta derived from different calf-production methods

In ruminants, overgrowth of offspring produced by in vitro fertilization (IVF) is a common problem. Abnormal epigenetic modifications caused by environmental factors during the early embryonic period are suspected as an etiology of overgrowth. In this study, we investigated the genome-wide histone H3K4me3 profiles of bovine placentae that play a pivotal role in fetal development and compared their characteristics between artificial insemination (AI)- and IVF-derived samples. Cotyledons were harvested from the placentae obtained at parturition of 5 AI- and 13 IVF-derived calves, and chromatin immunoprecipitation sequencing was performed for H3K4me3. We confirmed no significant maternal tissue contamination in the samples we used. The revealed H3K4me3 profiles reflected the general characteristics of the H3K4me3 modification, which is abundantly distributed in the promoter region of active genes. By extracting common modifications from multiple samples, the genes involved in placenta-specific biological processes could be enriched. Comparison with the H3K4me3 modifications of blastocyst samples was also effective for enriching the placenta-specific features. Principal component analysis suggested the presence of differential H3K4me3 modifications in AI- and IVF-derived samples. The genes contributing to the difference were related to the developmental biological processes. Imprinted genes such as BEGAIN, ZNF215, and DLX5 were among the extracted genes. Principal component and discriminant analyses using only male samples categorized the samples into three groups based on fetal weight and calf-production methods. To our knowledge, this is the first study to profile the genome-wide histone modifications of bovine fetal placentae and reveal their differential characteristics between different calf-production methods.

genomics↗

Exploring the genetic diversity of the Japanese Population: Insights from a Large-Scale Whole Genome Sequencing Analysis

The Japanese archipelago is a terminal location for human migration, and the contemporary Japanese people represent a unique population whose genomic diversity has been shaped by multiple migrations from Eurasia. Through high-coverage whole-genome sequencing (WGS) analysis of 9,850 samples from the National Center Biobank Network, we analyzed the genomic characteristics that define the genetic makeup of the modern Japanese population from a population genetics perspective. The dataset comprised populations from the Ryukyu Islands and other parts of the Japanese archipelago (Hondo). Low frequency detrimental or pathogenic variants were found in these populations. The Hondo population underwent two episodes of population decline during the Jomon period, corresponding to the Late Neolithic, and the Edo period, corresponding to the Early Modern era, while the Ryukyu population experienced a population decline during the shell midden period of the Late Neolithic in this region. Genes related to alcohol and lipid metabolism were affected by positive natural selection. Two genes related to alcohol metabolism were found to be 12,500 years out of phase with the time when they began to be affected by positive natural selection; this finding indicates that the genomic diversity of Japanese people has been shaped by events closely related to agriculture and food production. Author summaryThe human population in the Japanese archipelago exhibits significant genetic diversity, with the Ryukyu Islands and other parts of the archipelago (Hondo) having undergone distinct evolutionary paths that have contributed to the genetic divergence of the populations in each region. In this study, whole genome sequencing of healthy individuals from national research hospital biobanks was utilized to investigate the genetic diversity of the Japanese population. Haplotypes were inferred from the genomic data, and a thorough population genetic analysis was conducted. The results indicated not only genetic differentiation between Hondo and the Ryukyu Islands, but also marked differences in past population size. In addition, gene genealogies were inferred from the haplotypes, and the patterns were scrutinized for evidence of natural selection. This analysis revealed unique traces of natural selection in East Asian populations, many of which were believed to be linked to dietary changes brought about by agriculture and food production.

genomics↗

Molecular engineering of emicizumab to improve hemophilia A treatment

Emicizumab, a factor (F)VIIIa-function mimetic bispecific antibody (BsAb) to FIXa and FX, has become an indispensable treatment for people with hemophilia A (PwHA). Although emicizumab is very potent, long-term outcomes from the clinical studies suggest that a small proportion of PwHA still experiences bleeds. Additionally, non-clinical studies indicate that the maximum cofactor activity of emicizumab is lower than international standard activity (100 IU/dL of FVIII). An increased cofactor activity BsAb would benefit such patients. Here, we report NXT007, a BsAb binding FIXa and FX developed through further engineering of emicizumab. Emicizumab has a common light chain, but through advances in antibody engineering, we were able to create a more potent BsAb with two new non-common light chains. After extensive optimization of the heavy and light chains, the resulting BsAb, NXT007, exerted in vitro thrombin generation (TG) activity in hemophilia A plasma equivalent to 100 IU/dL of FVIII when triggered by tissue factor. NXT007 demonstrated potent hemostatic activity in an acquired hemophilia A model in non-human primates at a much lower dosage than emicizumab, consistent with an around 30-fold dose shift in the in vitro TG activity between NXT007 and emicizumab. Moreover, together with Fc engineering that enhanced FcRn binding and reduced in vivo clearance, we demonstrate that NXT007 could be effective at a much lower dosage with a longer dosing interval compared to emicizumab. These non-clinical results suggest that NXT007 could maintain a non-hemophilic range of coagulation potential in PwHA and provides a rationale for its clinical testing.

bioengineering↗

Droplet array-based platform for parallel optical analysis of dynamic extracellular vesicle secretion from single cells

Extracellular vesicles (EVs) are essential intercellular communication tools, but the regulatory mechanisms governing heterogeneous EV secretion are still unclear due to the lack of methods for precise analysis. Monitoring the dynamics of secretion from individually isolated cells is crucial because, in bulk analysis, secretion activity can be perturbed by cell-cell interactions, and a cell population rarely performs secretion in a magnitude- or duration-synchronized manner. Although various microfluidic techniques have been adopted to evaluate the abundance of single-cell-derived EVs, none can track their secretion dynamics continually for extended periods. Here, we have developed a droplet array-based method that allowed us to optically quantify the EV secretion dynamics of >300 single cells every 2 hours for 36 hours, which covers the cell doubling time of many cell types. The experimental results clearly show the highly heterogeneous nature of single-cell EV secretion and suggest that cell division facilitates EV secretion, showing the usefulness of this platform for discovering EV regulation machinery.

bioengineering↗

Semaphorin 3G exacerbates joint inflammation through the accumulation and proliferation of macrophages in the synovium

ObjectiveMethotrexate (MTX) is an anchor drug for rheumatoid arthritis (RA) treatment; however, the exact mechanisms by which MTX improves RA activity are still debatable. This study aimed to understand the roles of molecules whose expression is affected by MTX in RA patients and find novel therapeutic targets. MethodsCD4+ T cells from 28 treatment naive RA patients before and 3 months after the initiation of MTX treatment were subjected to DNA microarray analyses. The expression of Semaphorin 3G (Sema3G), as one of the differentially-expressed genes, and its receptor, Neuropilin-2 (Nrp2), was evaluated in RA synovium and collagen-induced arthritis (CIA) synovium. CIA and collagen antibody-induced arthritis (CAIA) were induced in Sema3G-deficient (Sema3G-/-) mice and control mice, and the clinical score, histological score, and serum cytokines were assessed. The migration and proliferation of Sema3G-stimulated bone marrow-derived macrophages (BMMs) were analyzed in vitro. The effect of local Sema3G administration during CAIA on the clinical score and the quantity of infiltrating macrophages was evaluated. ResultsThe expression of Sema3G in CD4+ T cells was downregulated by MTX treatment in RA patients. Sema3G was expressed in RA but not osteoarthritis synovium, and its receptor Nrp2 was mainly expressed on activated macrophages. Sema3G deficiency ameliorated CIA and CAIA. Sema3G stimulation enhanced the migration and proliferation of BMMs. The local administration of Sema3G deteriorated CAIA and increased infiltrating macrophages. ConclusionsUpregulation of Sema3G in RA synovium is a novel mechanism to deteriorate joint inflammation through the accumulation of macrophages. Key messagesSemaphorin 3G is expressed in the inflamed synovium in human and mice. The receptor of Semaphorin 3G is mainly expressed on M1 macrophages. Semaphorin 3G deteriorates inflammatory arthritis through macrophage proliferation and migration.

pathology↗