Biology subjects

Fujimori, T.

Publications and source records attributed to Fujimori, T..

At least 19 recordsLinked to original sources

bioRxiv2026

A multimodal perturbation atlas defines the phenotypic resolution of cellular morphology.

Modeling cellular behavior requires measurements that capture how cells evolve across time, environments, and interventions. Microscopy is uniquely suited to this goal: it is non-destructive and can be applied to living cells in their native context. Yet its phenotypic resolving power remains incompletely characterized relative to molecular assays. Here, we present a multimodal perturbation atlas of 1,000 pooled CRISPR knockouts in A549 cells, profiled by fluorescence microscopy (42 live, 13 fixed markers), label-free quantitative phase imaging of the same live cells (at single timepoints), and single-cell RNA sequencing (scRNA-seq). We develop deep learning frameworks to interpret the rich cell-biological signatures in these ~65M single-cell profiles. At matched reagent cost, phase imaging exceeds the phenotypic resolution of both fluorescence imaging and scRNA-seq, and more reliably recovers higher-order pathway organization. These results establish intrinsic morphology as a high-precision readout of cellular state, and lay a foundation for live-cell profiling of phenotypic trajectories.

systems biology↗

bioRxiv2026

The association of extracellular vesicle (EV)-cargo miR-330-3p with postoperative delirium and a potential mechanism of tau phosphorylation and neuron toxicity

BackgroundPostoperative delirium (POD) is a frequent and severe neurocognitive complication following cardiac surgery, associated with poor long-term outcomes. The underlying mechanisms are unclear, and objective biomarkers are urgently needed. MethodsWe used pre- and post-operative plasma samples from 59 patients undergoing cardiac surgery in three separate studies with rigorous delirium assessment using the Confusion Assessment Method in a case-control design. Small extracellular vesicles (sEVs) were isolated from plasma, and their miRNA cargo was profiled using RNA sequencing. Target miRNAs were validated by qRT-PCR, and digital PCR (dPCR). The functional impact of the lead candidate miRNA was investigated in vitro by assessing tau phosphorylation and cell viability in HT22 neuronal cell line. ResultsThere were no differences in sEV morphology or numbers between patients with and without POD. While three candidate miRNAs were initially validated by qRT-PCR, subsequent dPCR analysis confirmed that only the perioperative change in plasma sEV-cargo miR-330-3p expression was significantly greater in patients who developed POD (n = 20) compared with those who did not (n = 20) (5.22 copies/L plasma; 95% Confidence Interval (CI), 1.187 to 9.256; p = 0.0139). Receiver operating characteristic curve analysis for this change yielded an area under the curve of 0.745 (95% CI, 0.589 to 0.901). In vitro overexpression of miR-330-3p in a neuronal cell line significantly increased the phosphorylation of tau at Ser199 (p < 0.0001) and Ser396 (p < 0.001) and reduced cell viability (p < 0.001). ConclusionsOur findings suggest that sEV-bound miR-330-3p increases in patients with POD after cardiac surgery. In vitro results suggest a potential pathogenic role for miR-330-3p, linking a systemic signal to tau-related neuronal injury. Clinical PerspectiveO_ST_ABSWhat Is New?C_ST_ABSO_LIThis study identifies a specific perioperative increase in small extracellular vesicle (sEV)-cargo miR-330-3p in patients with postoperative delirium (POD) following cardiac surgery. C_LIO_LIWe provide the first evidence that miR-330-3p directly induces tau hyperphosphorylation and reduces neuronal viability in vitro, establishing a potential mechanistic link between systemic sEV signaling and neurodegeneration. C_LI What Are the Clinical Implications?O_LIThe measurement of perioperative change in miR-330-3p could serve as an objective biological marker to assist in the early identification and risk stratification of patients at high risk for POD. C_LIO_LIThe identified miR-330-3p/tau pathway represents a potential new therapeutic target; future interventions aimed at inhibiting this specific miRNA might help prevent or mitigate POD-related neuronal injury. C_LIO_LIThese findings emphasize the importance of monitoring dynamic sEV-cargo changes to better understand and manage perioperative neurocognitive disorders. C_LI

molecular biology↗

bioRxiv2026

Mechanically competitive regulation of cell volume in cytoplasm-sharing cells connected by intercellular bridges

In multicellular organisms, various cellular structures exhibit cytoplasmic sharing, where cells remain interconnected. While essential for development and function in contexts such as germ cell formation and insect early embryos, the physical basis of cell volume regulation in these systems remains poorly defined. Germline cysts are formed by interconnected sister cells via intercellular bridges. In mice, germline cysts form during gametogenesis in fetal ovaries and testes. In mouse fetal female cysts, cells with numerous bridges preferentially differentiate into oocytes by selectively increasing their volume, a process that may be mediated through cytoplasmic flow. This volume bias may be influenced by hydrostatic pressure within the cytoplasm. Here, we theoretically investigate how the mechanical properties of cells affect cytoplasmic pressure and volume distribution within interconnected cells. Our soap-bubble model revealed that cells with more bridges exhibit increased volume when they have large cell-cell contact areas, as observed in fetal cysts. We found that incorporating cell cycle (including cell growth and cell division) significantly enhances the likelihood of volume bias in favor of cells with more bridges. These theoretical findings suggest that intrinsic mechanical properties, coupled with cell cycle, establish robust cyst development in fetal female germline cysts. Our findings also provide insights into the volume dynamics observed in adult male germline cysts, which are characterized by smaller cell-cell contact areas. Impact statementA theoretical model demonstrates how mechanical properties and cell cycle dynamics regulate volume distribution in germline cysts, providing a physical basis for oocyte differentiation.

developmental biology↗

bioRxiv2025

Bifunctional transcriptional effector domains control gene expression pulses in an occupancy-dependent manner

Dynamic gene expression pulses enable adaptive response to stimuli and can be generated in natural and synthetic systems. Controlling these dynamics typically involves circuits consisting of multiple genes and transcription factors (TFs). Here, we discover a new class of bifunctional transcriptional effector domains that can first activate and subsequently repress the same gene, producing dynamic gene expression pulses from a single input. These pulse dynamics arise from distinct, temporally separated chromatin states defined by active and repressive chromatin modifications. The balance between active and repressed states is determined by the DNA occupancy of the bifunctional TF. Bifunctional domains activate at low occupancy but switch to repression at high occupancy, resulting in a non-monotonic TF input-gene expression output relationship tunable by TF concentration and number of DNA binding sites. We develop a kinetic model that links TF occupancy to gene expression transitions, allowing for the programming of eight distinct cell "states" - combinations of On/Off states of 3 reporter genes - using a single bifunctional effector. This work establishes the theoretical framework and molecular mechanisms of pulse-generating gene regulation by bifunctional domains and creates a foundation for engineering complex multi-gene circuits.

systems biology↗

bioRxiv2025

MAP7-driven cytoskeletal cross-talk establishes Sertoli cell polarity crucial for germ cell meiotic progression

How specialized apical membrane domains are assembled in vivo remains poorly understood. In the mouse testis, Sertoli cells build a luminal apical domain after birth that organizes the seminiferous epithelium and supports germ cell differentiation, distinct from fetal polarity established during cord formation. Here, we identify the microtubule-associated protein MAP7 as a key regulator of cytoskeletal organization during apical domain formation. MAP7 preferentially localizes to apical microtubules in Sertoli cells, showing limited overlap with stable microtubule markers. Native-tissue imaging indicates that MAP7-decorated microtubules, initially lacking obvious directionality, become increasingly aligned along the tubule axis as the apical domain matures. In Map7-deficient testes, microtubule abundance is maintained, but higher-order organization is disrupted and accompanied by persistent luminal F-actin accumulation. These defects compromise apical domain maturation and lumen formation during the first wave of spermatogenesis and are associated with altered tight-junction patterning. Proteomic analysis identifies the non-muscle myosin II heavy chains MYH9 and MYH10 among MAP7-associated proteins. MYH9 becomes enriched at luminal regions where microtubules and F-actin converge, but remains diffuse in Map7-deficient Sertoli cells despite ectopic luminal cytoskeletal assemblies, suggesting that MAP7 helps establish a cytoskeletal context that supports spatially restricted NMII enrichment. Single-cell RNA sequencing shows that Sertoli transcriptional differentiation largely proceeds without MAP7, whereas germ cells exhibit delayed meiotic progression with expansion of pachytene-stage subpopulations. Together, these findings establish MAP7-dependent microtubule remodeling as an organizing mechanism for postnatal apical domain maturation and suggest how epithelial cytoskeletal architecture shapes a niche that helps pace developmental progression of neighboring germ cells.

cell biology↗

bioRxiv2025

Emergence of cell polarity by reciprocal interactions between Wnt and core PCP components

Planar cell polarity (PCP) is established by asymmetric localization of core PCP components in each cell. Since some Wnt proteins can induce PCP in vertebrates, it has been proposed that Wnt concentration gradients provide spatial cues for polarization. Here, however, we present evidence that Wnt11 can regulate PCP in a gradient-independent manner. In the neural plate of Xenopus embryos, endogenous Wnt11 does not form an obvious gradient in the direction of PCP, but is polarized at cell boundaries together with core PCP components. Wnt11 polarization is dependent on core PCP components, while polarization of core PCP components can also be induced by Wnt11, indicating a mutual amplification loop between Wnt11 and core PCP components in PCP formation. Furthermore, Wnt11 and core PCP components compose an intercellular loop to coordinate the direction of polarity. Thus, we propose that local and reciprocal interactions between Wnt11 and core PCP components can generate PCP.

developmental biology↗

bioRxiv2025

An antiparallel cell circulation driven by self-alignment induces phase separation

Active tissues exhibit diverse collective dynamics, yet the cell-cell interactions that generate ordered microscopic flows remain poorly understood. Here, we show that antiparallel cell circulation can emerge from self-aligned, polarity-dependent tension gradients. Using a minimal vertex model of confluent tissues, we studied polar cells that align their polarity with their own velocity and impose polarity-dependent tension gradients along cell-cell contacts, without relying on substrate traction. This behavior can be generalized as a minimal interaction in which forces transmitted between cells act with opposite signs, reminiscent of action-reaction forces, organizing cells into stable interlocking antiparallel lanes. In mixtures of motile and nonmotile cells, this circulation drives phase separation, in which motile cells spontaneously form persistent domains. Accordingly, we identified similar antiparallel circulation patterns in two-dimensional aggregates of Dictyostelium discoideum, supporting the biological relevance of the mechanism. Together, these results demonstrate that self-aligned tension gradients provide a robust and underappreciated route to dynamic microscopic pattern formation in multicellular systems.

biophysics↗

bioRxiv2025

Directional alignment of different cell types organizes planar cell polarity

Planar cell polarity (PCP) refers to unidirectional coordination of cell polarity in the plane of epithelial tissues, whose proper formation is essential for development in various tissues. While imbalances in the amount of core PCP proteins (core proteins) between adjacent cells disrupt PCP in some tissues, other tissues maintain PCP despite containing multiple cell types with different levels of core proteins. How such tissues tolerate these imbalances remains unclear. Here, we theoretically analyzed the contribution of spatial distribution of different cell types to PCP maintenance. We adopted a previously established PCP model on two-dimensional cell sheets, where local protein-protein interactions were assumed. Our systematic simulations revealed that the patterns of cell-type distribution significantly affect the accuracy of PCP maintenance under the condition of imbalanced PCP proteins. To identify the critical patterns, we applied both deep learning techniques and statistical modeling to the simulation data. Consequently, these analyses revealed that orientation of cell-type alignment is a key aspect of cell-type distribution that affects PCP. Such directional cell-type alignment was observed in the mouse oviduct. Our findings highlight the overlooked contribution of spatial distribution of cell types to PCP maintenance in tissues with multiple cell-types.

developmental biology↗

bioRxiv2025

Inducible degradation of endogenous proteins by AlissAID system and development of a photoactivatable inducer.

Protein analysis strategies involving targeted protein degradation are powerful approaches to determine gene functions. Auxin-inducible degron (AID) is among the most widely used methods for target protein knockdown. This system enables the rapid depletion of AID-tagged target proteins in an auxin-dependent manner. Various improved AID methods have been developed to date; however, the requirement to tag the target protein remains a common challenge. Here, we demonstrated the efficiency of the affinity-linker-based super-sensitive AID system for condition-knockdown of target proteins in cultured animal cells and mouse embryos. This system combines the improved AID method with small-molecule antibodies, enabling the control of GFP and mCherry fusion proteins. Additionally, this system can be used to degrade endogenous targets, such as Ras proteins. We also developed a novel inducer, caged 5-adamantyl-IAA, that precisely controlled targeted protein degradation under light irradiation. This advanced technique aids in the degradation of endogenous proteins of interest and can be used to develop new technologies for localized protein degradation.

cell biology↗

bioRxiv2025

Competitive elimination of ZO-1/ZO-2-deficient cells regulates epithelial barrier homeostasis

Epithelia cover the body and form a barrier to segregate the internal body from the external environment. Epithelial tissues contact the external environment and are exposed to various stresses that are potentially deleterious for the epithelial barrier1. However, how focal epithelial barrier defects are detected and repaired to maintain epithelial barrier homeostasis remains poorly understood. We co-cultured ZO-1/ZO-2 double-knockout (DKO) MDCK II cells, which lack tight junctions, with wild-type MDCK II cells, to understand how epithelial cells respond to focal epithelial barrier defects. When co-cultured with wild-type cells, ZO-1/ZO-2 DKO cells were selectively eliminated by induction of apoptosis. The elimination depended on a purse-string-like contraction of supracellular actomyosin cables formed at the clone boundary, regulated by ROCK. Furthermore, Hippo signaling and adherens junctions in the surrounding wild-type cells were required to eliminate ZO-1/ZO-2 DKO cells. These results demonstrate that selective elimination of ZO-1/ZO-2-deficient cells by cell competition regulates epithelial barrier homeostasis. In briefOtani et al. reveal that epithelial barrier homeostasis is regulated by cell competition-mediated elimination of ZO-1/ZO-2-deficient cells. Supracellular actomyosin cables form at the clone boundary and constrict in a purse-string-like manner to eliminate the loser cells. Mechanosensing in the winning cells is required to eliminate the loser cells. HighlightsO_LIZO-1/ZO-2-deficient cells are eliminated by cell competition C_LIO_LIActomyosin cables form in the winning cells at the clone boundary C_LIO_LIA purse-string-like contraction of actomyosin cables compresses the losing cells C_LIO_LIMechanosensing in the winning cells is important to eliminate the loser cells C_LI

cell biology↗

bioRxiv2024

Cell position-based evaluation of mechanical features of cells in multicellular systems

Measurement of mechanical forces of cell-cell interactions is important for studying the emergence of diverse three-dimensional morphologies of multicellular organisms. We previously reported an image-based statistical method for inferring effective pairwise forces of cell-cell interactions (i.e., attractive/repulsive forces), where a cell particle model was fitted to cell tracking data acquired by live imaging. However, because the particle model is a coarse-grained model, it remains unclear how the pairwise forces relates to sub-cellular mechanical components including cell-cell adhesive forces. Here we applied our inference method to cell tracking data generated by vertex models that assumed sub-cellular components. Through this approach, we investigated the relationship between the effective pairwise forces and various sub-cellular components: cell-cell adhesion forces, cell surface tensions, cell-extracellular matrix (ECM) adhesion, traction forces between cells and ECM, cell growth, etc. We found that the cell-cell adhesion forces were attractive, and both the cell surface tensions and cell-ECM adhesive forces were repulsive, etc. These results indicate that sub-cellular mechanical components can contribute to the effective attractive/repulsive forces of cell-cell interactions. This comprehensive analysis provides theoretical bases for linking the pairwise forces to the sub-cellular mechanical components: this showcase is useful for speculating the sub-cellular mechanical components from the information of cell positions, and for interpreting simulation results based on particle models.

biophysics↗

bioRxiv2024

CENP-C-Mis12 complex establishes a regulatory loop through Aurora B for chromosome segregation

Establishing the correct kinetochore-microtubule attachment is crucial for faithful chromosome segregation. The kinetochore has various regulatory mechanisms for establishing correct bipolar attachment. However, how the regulations are coupled is not fully understood. Here, we demonstrate a regulatory loop between the kinetochore protein CENP-C and Aurora B kinase, which is critical for the error correction of kinetochore-microtubule attachment. This regulatory loop is mediated through the binding of CENP-C to the outer kinetochore Mis12 complex (Mis12C). Although the Mis12C binding region of CENP-C is dispensable for mouse development and proliferation in human RPE-1 cells, those cells lacking this region display increased mitotic defects. The CENP-C-Mis12C interaction facilitates the centromeric recruitment of Aurora B and the mitotic error correction in human cells. Given that Aurora B reinforces the CENP-C-Mis12C interaction, our findings reveal a positive regulatory loop between Aurora B recruitment and the CENP-C-Mis12C interaction, which ensures chromosome bi-orientation for accurate chromosome segregation.

cell biology↗

bioRxiv2023

Mechanical transapical coupling of endometrial epithelial cells during implantation

Epithelial cells lining the lumen of organs have an apical-basal polarity, and mechanical cell contacts are located in the lateral and basal regions. During early pregnancy in rodents, the luminal space of the uterus is closed, and opposing epithelial cells attach to each other at apical-apical surfaces. Here, we show that cells are mechanically coupled at the apical cell-cell contacts. The apical plasma membrane was intricately intertwined between opposing cells. Extracellular matrix and tight junction molecules were localized at apical contacts. Claudin inhibition resulted in impaired luminal closure, suggesting a functional requirement of claudins for the establishment of transapical coupling. The present results demonstrate a mechanical cell-cell interaction that occurs between apical-apical surfaces in addition to lateral and basal cell junctions. One Sentence SummariesTransapical coupling of epithelial cells mediated by extracellular matrix and tight junction molecules

cell biology↗

bioRxiv2023

Single-cell chromatin state transitions during epigenetic memory formation

Repressive chromatin modifications are thought to compact chromatin to silence transcription. However, it is unclear how chromatin structure changes during silencing and epigenetic memory formation. We measured gene expression and chromatin structure in single cells after recruitment and release of repressors at a reporter gene. Chromatin structure is heterogeneous, with open and compact conformations present in both active and silent states. Recruitment of repressors associated with epigenetic memory produces chromatin compaction across 10-20 kilobases, while reversible silencing does not cause compaction at this scale. Chromatin compaction is inherited, but changes molecularly over time from histone methylation (H3K9me3) to DNA methylation. The level of compaction at the end of silencing quantitatively predicts epigenetic memory weeks later. Similarly, chromatin compaction at the Nanog locus predicts the degree of stem-cell fate commitment. These findings suggest that the chromatin state across tens of kilobases, beyond the gene itself, is important for epigenetic memory formation.

genetics↗

bioRxiv2023

Effective mechanical potential of cell-cell interaction in tissues harboring cavity and in cell sheet toward morphogenesis

Measuring mechanical forces of cell-cell interactions is important for studying morphogenesis in multicellular organisms. We previously reported an image-based statistical method for inferring effective mechanical potentials of pairwise cell-cell interactions by fitting cell tracking data with a theoretical model. However, whether this method is applicable to tissues with non-cellular components such as cavities remains elusive. Here we evaluated the applicability of the method to cavity-harboring tissues. Using synthetic data generated by simulations, we found that the effect of expanding cavities was added to the pregiven potentials used in the simulations, resulting in the inferred effective potentials having an additional repulsive component derived from the expanding cavities. Interestingly, simulations by using the effective potentials reproduced the cavity-harboring structures. Then, we applied our method to the mouse blastocysts, and found that the inferred effective potentials can reproduce the cavity-harboring structures. Pairwise potentials with additional repulsive components were also detected in two-dimensional cell sheets, by which curved sheets including tubes and cups were simulated. We conclude that our inference method is applicable to tissues harboring cavities and cell sheets, and the resultant effective potentials are useful to simulate the morphologies.

biophysics↗

bioRxiv2023

Tight junction membrane proteins regulate the mechanical resistance of the apical junctional complex

Epithelia must be able to resist mechanical force to preserve tissue integrity. While intercellular junctions are known to be important for the mechanical resistance of epithelia, the roles of tight junctions (TJs) remain to be established. We previously demonstrated that epithelial cells devoid of the TJ membrane proteins claudins and JAM-A completely lack TJs and exhibit focal breakages of their apical junctions. Here, we demonstrate that apical junctions undergo spontaneous fracture when claudin/JAM-A-deficient cells are exposed to mechanical stress. The junction fracture was accompanied by actin disorganization, and actin polymerization was required for apical junction integrity in the claudin/JAM-A-deficient cells. Further deletion of CAR resulted in the disruption of ZO-1 molecule ordering at cell junctions, accompanied by severe defects in apical junction integrity. These results demonstrate that TJ membrane proteins regulate the mechanical resistance of the apical junctional complex in epithelial cells. SummaryTight junction membrane proteins claudins, JAM, and CAR coordinately regulate the nanometer-scale organization of ZO-1 molecules, and are required for the mechanical resistance of apical junctions in epithelial cells.

cell biology↗

bioRxiv2023

Discovery of the apiosyltransferase, celery UGT94AX1 that catalyzes the biosynthesis of a flavone glycoside, apiin

Apiose is a unique branched-chain pentose found in plant glycosides and a key component of the cell wall-polysaccharide pectin and other specialized metabolites. More than 1,200 plant-specialized metabolites contain apiose residues, represented by apiin, a distinctive flavone glycoside found in celery and parsley in the family Apiaceae. The physiological functions of apiin remain obscure, partly due to our lack of knowledge on apiosyltransferase during apiin biosynthesis. Here, we identified celery UGT94AX1 (AgApiT) as a novel apiosyltransferase, responsible for catalyzing the last sugar-modification step in apiin biosynthesis. AgApiT showed strict substrate specificity for the sugar donor, UDP-apiose, and moderate specificity for acceptor substrates, thereby producing various apiose-containing flavone glycosides in celery. Homology modeling of AgApiT with UDP-apiose, followed by site-directed mutagenesis experiments, identified unique Ile139, Phe140, and Leu356 residues in AgApiT, which are seemingly crucial for the recognition of UDP-apiose in the sugar donor pocket. Sequence comparison and molecular phylogenetic analysis of celery glycosyltransferases paralogous to AgApiT suggested that AgApiT is the sole apiosyltransferase-encoding gene in the celery genome. This is the first report on the identification of a plant apiosyltransferase gene that will enhance our understanding of the physio-ecological functions of apiose and apiose-containing compounds.

biochemistry↗

bioRxiv2022

An ImageJ-based tool for three-dimensional registration between different types of microscopic images

Three-dimensional (3D) registration (i.e. alignment) between two microscopic images is substantially helpful to study tissues not adhere to substrates such as mouse embryos and organoids which are often three-dimensionally rotated during imaging. However, there is no 3D registration tool easily accessible for experimental biologists. Here we developed an ImageJ-based tool which achieves 3D registration accompanying both quantitative evaluation of the accuracy and reconstruction of 3D rotated images. In this tool, several landmarks are manually provided in two images to be aligned, and 3D rotation is computed so that the distances between the paired landmarks from the two images are minimized. By simultaneously providing multiple points (e.g. all nuclei in the regions of interest) other than the landmarks in the two images, the correspondence of each point between the two images is quantitatively explored: a certain nucleus in one image corresponds to which nucleus in another image. Furthermore, the 3D rotation is applied to one of the two images, resulting in reconstruction of 3D rotated images. We demonstrated that this tool successfully achieved 3D registration and reconstruction of images in mouse pre-implantation embryos, where one image was obtained during live imaging and another image from fixed embryos after live imaging. This approach provides a versatile tool applicable for various tissues and species.

developmental biology↗