Biology subjects

Kondo, Y.

Publications and source records attributed to Kondo, Y..

At least 19 recordsLinked to original sources

bioRxiv2026

Spatially resolved mapping of tau amplification rates via differentiable simulation of prion-like propagation

Neurodegenerative diseases exhibit characteristic yet heterogeneous patterns of pathological spread, whose underlying determinants remain unclear. A central challenge is that inferring spatially heterogeneous propagation kinetics from neuroimaging data constitutes a high-dimensional inverse problem that has remained intractable at the whole-brain scale. Here, we present a differentiable reaction-diffusion framework that enables inference of spatially resolved tau amplification rates from tau PET data. By integrating MRI-informed forward simulation with error backpropagation, our approach reconstructs subject-specific voxel-wise maps of tau amplification rates across the human brain. Analysis of the inferred maps showed that the amplification rates have a positive spatial association with amyloid PET, suggesting that they capture aspects of regional vulnerability to amyloid-driven tau accumulation. Furthermore, integration with transcriptomic data identified gene expression programs associated with regional variation in amplification. These findings provide a data-driven framework linking molecular architecture to large-scale propagation dynamics in neurodegeneration.

neuroscience↗

bioRxiv2026

Circulating miR-1285-3p promotes age-associated B cell differentiation through the OXPHOS-IKZF2 axis in SLE

Age-associated B cells (ABCs) expand in systemic lupus erythematosus (SLE) and contribute to pathogenic humoral immunity, but the mechanisms that restrain their differentiation remain unclear. Here, we identify the transcription factor IKZF2 (Helios) as a regulator that limits ABC differentiation. Transcriptomic and functional analyses showed that suppression of oxidative phosphorylation (OXPHOS) in B cells promoted ABC differentiation and was accompanied by reduced IKZF2 expression. Pharmacologic modulation of mitochondrial metabolism further demonstrated that OXPHOS inhibition promoted, whereas OXPHOS activation restrained, ABC differentiation. Integrative analyses revealed reduced IKZF2 expression in selected B cell subsets from patients with SLE. Functional suppression of IKZF2 enhanced ABC differentiation and attenuated the inhibitory effects of OXPHOS activation, indicating that IKZF2 mediates metabolic control of B cell fate. Mechanistically, IKZF2 restrained early ABC-associated gene programs, including ITGAX and TBX21. Circulating miR-1285-3p in small extracellular vesicles, elevated in SLE, suppressed OXPHOS and recapitulated these effects. Together, these findings identify an OXPHOS-IKZF2 axis that restrains pathogenic B cell differentiation and links extracellular microRNA-mediated metabolic stress to ABC formation in SLE. One-sentence summarySmall EV-associated miR-1285-3p in SLE promotes ABC differentiation by suppressing OXPHOS and relieving IKZF2-mediated restraint.

immunology↗

bioRxiv2026

Elasticity of a three-dimensional cell vertex model of epithelia

Material properties of epithelial tissues play essential roles in morphogenesis and physiological function, yet how tissue-scale viscoelasticity emerges from cellular-scale mechanics remains unclear. Here, we investigate the elastic mechanics of a three-dimensional cell vertex model for epithelial monolayers. By analyzing infinitesimal affine deformations around a regular hexagonal-prism equilibrium state, we derive analytical expressions for the in-plane elastic moduli. We show that the model produces a near-zero in-plane Poissons ratio over a broad region of parameter space, thereby accounting for a characteristic mechanical property reported in cultured epithelial monolayers. Numerical simulations further confirm that the theoretical Poissons ratio remains accurate under finite, biologically relevant strains. In addition, we show that the morphological bistability between squamous-like and columnar-like states is associated with distinct elastic responses. Our results indicate that three-dimensional vertex models can account not only for epithelial morphogenesis but also for their material properties.

biophysics↗

bioRxiv2026

Inferring division-associated stochasticity from time-series single-cell transcriptomes

Cell division is fundamental to multicellular organisms and stochastic partitioning of cellular components can strongly affect genome-wide gene expression states. However, how cell division-associated partitioning noise shapes the dynamics of proliferating cells is poorly understood. Here, we propose scDIVIDE, a neural stochastic differential equation framework to infer continuous cellular dynamics and division rates while accounting for partitioning noise. We combined birth-death-mutation processes from population genetics with dynamical optimal transport and revealed that the birth rate is embedded in the diffusion coefficient, enabling its inference from time-series scRNA-seq data. scDIVIDE accurately inferred birth rates in synthetic data and the inferred birth rates recapitulated turnover-related programs in mouse hematopoiesis data. By exploiting the birth-diffusion coupling, scDIVIDE provides a biologically-informed constraint on growth rate estimation, outperforming existing methods in predicting future cell distributions. scDIVIDE provides a conceptual avenue for quantitatively dissecting how partitioning noise shapes fate decisions in multicellular systems.

bioinformatics↗

bioRxiv2026

Filament-resolved simulations reproduce self-organization of lamellipodia and filopodia

The dynamic assembly of actin filaments underlies diverse cellular morphologies such as lamellipodia, filopodia, and reticulated networks. However, how filament-scale interactions among actin-binding proteins produce distinct actin architectures remains unclear. We developed a filament-resolved computational model of actin self-organization regulated by the Arp2/3 complex and fascin. Individual F-actin filaments are represented as elastic chains, and their stochastic polymerization, Arp2/3-mediated branching, and fascin-mediated crosslinking and bundling are explicitly modeled. The simulations reproduce three actin architectures observed in minimal reconstitution experiments, including lamellipodia-like branched networks, filopodia-like bundled protrusions, and reticulated meshworks, as a function of Arp2/3 and fascin concentrations. We quantify these regimes using actin density, orientational order, and spikiness, which robustly separate the three morphologies across conditions. To connect filament organization to shape change, we further couple the actin network to membrane deformation using a phase-field formulation. This coupling shows how localized remodeling concentrates load to drive pseudopodial protrusions, whereas highly branched networks distribute stresses and stabilize rounded shapes. The model links molecular interactions to emergent architecture and cell-scale morphodynamics.

biophysics↗

bioRxiv2025

A New anticancer substance from cancer cell apoptosis. CSS (Cancer cell Suicide Substance) production in culture.

It is well-known that the cells die when a cancer cell line is continuously cultured without passage, even though it was kept in a fresh medium. However, none of this phenomenons decisive causes and mechanism(s) have been elucidated yet. After the cancer cell death, the medium exserted cytocidality. This cancer cell death (e.g., spontaneous, apoptosis, programmed) was found to be caused by only one kind of cytocidal substance (MW<1kDa) (named CSS) produced from the cells own component(s) by the cells themselves. CSS mammalian specifically by cancer cell lines but not nontumor cell lines and the CSS exerted cytocidality against other cell lines and vice versa regardless of species in mammalian. In vivo, CSS showed a significant life-prolonging effect without any adverse event. An established cell line derived from human renal cell carcinoma (HRC23) was used in this study as CSS was found and characterized by this cell line first. HighlightsO_LIOnly one kind of low molecular substance exerting cytocidality was found only in a medium after cancer cells death in the culture but not in non-tumor cell lines one. C_LIO_LIThe cytocidal substance (named CSS: cancer cell suicide substance) was a small molecule (MW<1kDa) with a slightly positively charged highly hydrophilic character. C_LIO_LICSS was produced regardless of extracellular nutritional condition, even in glucose-free HBSS (Nutrition-Free Method.) C_LIO_LICSS exserted cytocidality against other cancer cell lines irrespective of the histological patterns and the species of mammalian cells and vice versa. C_LIO_LICSS can be considered as a direct and critical substance produced from cell component(s) themselves by the cancer cells themselves. C_LIO_LIProduction of CSS was specific for cancer cells. This clear functional difference between cancer and nontumor cells should be meaningful embryologically. C_LIO_LIIn vivo, CSS showed complete anti-metastasis during administration period against Lewis Lung Carcinoma (LLC) transplanted mouse without any adverse event. CSS may have high potential as a new type of cancer therapy drug. C_LI In shortThis study is so simple, absolutely reproducible and anyone can reproduce this study with an easy basic method. A critical substance CSS (cancer cell suicide substance) of spontaneous cancer cell death was found in a medium after the cancer cells had been dead. Only one kind of small-size substance with MW<1kDa with a highly water-soluble and positively charged character is made only from cell own component(s) itself by the cells themselves. Even in a nutrition-free physiologically balanced salt solution, CSS was produced regardless of extracellular nutritional condition. Only cancer cell lines produced CSS, but not by non-tumor cell lines. CSS exserted cytocidality against other histologically different patterns of cancer cell lines regardless of species and vice versa. The anticancer effect of HRC23 produced CSS in vivo against mouse LLC (Lewis Lung Carcinoma)-transplanted mice showed a clear life-prolonging effect without any adverse event. Thus, CSS may have the possibility to be a cancer therapy drug. And, in view of embryologically, this clear difference of CSS production between cancer cells and nontumor cells will be important event.

cancer biology↗

bioRxiv2025

Mechanism of MEK1 phosphorylation by the N-terminal acidic motif mediated asymmetric BRAF dimer

The RAF/MEK/ERK signaling cascade regulates cell proliferation and differentiation and is frequently dysregulated in cancer. Approximately 90% of RAF-mutant cancers harbour mutations in B-type of Rapidly Accelerated Fibrosarcoma (BRAF). Its proto-oncogenicity has been attributed to a four-residue N-terminal acidic (NtA) motif. While a long-standing model proposes that the NtA promotes an activating asymmetric RAF dimerization, this idea has lacked structural support. Here, we present the first X-ray crystal structure of an NtA-mediated asymmetric BRAF dimer bound to its substrate Mitogen-activated Protein kinase Kinase (MEK1). Further cellular and biochemical analyses reveal that this asymmetric dimer is not an intermediate along the BRAF activation pathway, but rather a catalytically active state of the kinase. We validate this with the structure of BRAF bound to Ser222-phosphorylated MEK1, capturing the complex in a post-catalytic state. This combination of structural and cellular analysis establishes the relevance of NtA-driven asymmetry in BRAF activation and resolves a long-standing disconnect between RAF cancer genetics and structural biology.

biochemistry↗

bioRxiv2025

Inverse modeling unveils governing law of mechano-chemical dynamics of epithelial migration

Collective cell migration is fundamental to tissue homeostasis and underlies biological processes such as wound healing and cancer invasion. Previous work has proposed governing equations to describe how chemical and mechanical inputs regulate these movements, but the quantitative validity of such models remains to be thoroughly assessed. Here, we developed a machine-learning framework that infers the governing equation from live-cell imaging data. Applied to epithelial sheet migration driven by MAPK/ERK, our approach quantitatively predicted single-cell movement from local chemical and mechanical cues. Examination of the learned equations further indicated that cells process environmental signals by computing their spatiotemporal derivatives. Moreover, when applied to individual cells, our framework revealed cell-cell heterogeneity in the underlying migratory rules. Our framework offers a powerful tool for predictive modeling of multicellular dynamics in both physiological and pathological settings.

systems biology↗

bioRxiv2025

Time-resolved structures of β2-adrenergic receptor modulation by a photoswitchable beta-blocker

G protein-coupled receptors (GPCRs) regulate essential physiological responses and are important drug targets, yet their ligand-induced conformational dynamics remain poorly understood. The {beta}2-adrenergic receptor ({beta}2AR) is a prominent member of the GPCR family. It regulates bronchial and vascular function and is a significant drug target, particularly in respiratory and smooth muscle-related disorders. We employed time-resolved crystallography at X-ray free-electron lasers (XFELs) to capture the conformational dynamics of {beta}2AR bound to photoazolol-1, a beta-blocker derivative developed for photopharmacological applications. Structural snapshots of the receptor bound to trans-photoazolol-1 (pre-photoconversion), a strained intermediate, and the fully photoisomerized cis-photoazolol-1 reveal an intricate interplay between ligand chemistry and receptor plasticity. Isomerization of the azobenzene moiety induces distinct conformational changes within the orthosteric pocket, altering interactions with the extracellular loop 2 and transmembrane helices 5 and 6. Supported by functional assays, these structural shifts suggest that photoazolol-1 transitions from an inverse agonist to a neutral antagonist upon photoactivation. Our findings uncover a mechanism of GPCR modulation reminiscent of rhodopsin activation and offer a framework for designing ligands that harness light-driven transitions to achieve spatiotemporal control of receptor function.

biochemistry↗

bioRxiv2025

Intensity Modulation of Trichromatic Split Fluorescent Proteins for Live Cell Mapping

Multiplexed live cell-labeling technologies are essential tools for investigating complex biological systems, yet existing approaches face limitations in achieving reliable discrimination of multiple cell populations. Here, we present color and intensity modulation with split fluorescent proteins for cell labeling (Caterpie), a live cell labeling system that enables high-fidelity identification of multiple cell populations through rational design of split fluorescent proteins. Drawing inspiration from human trichromatic vision, we engineered optimized split fluorescent protein variants--split CFP2, split mNG3A, and split sfCherry3C--and developed a comprehensive library of the 11th {beta}-strand (FP11) tags comprising variable numbers of tandem repeats. Structure-guided protein engineering enhanced the performance of split mNG3A and split sfCherry3C through targeted modifications of their C-terminal sequences and binding interfaces, respectively. By systematically varying the composition and arrangement of FP11 repeats, we selected 20 distinct FP11 tags that enable robust cell population discrimination with 97% accuracy using conventional fluorescence microscopy. In these FP11 tag-expressing cells, we expressed multiple EGF ligands and their receptors and cultured them in bulk to examine the effects of EGF signaling on chemotaxis within the cell population. The results showed that chemotaxis changes according to the intensity of EGFR signaling. The Caterpie system holds significant potential for applications requiring precise identification and tracking of multiple cell populations in complex biological systems.

cell biology↗

bioRxiv2025

Inverse signal importance in real exposome: How do biological systems dynamically prioritize multiple environmental signals?

Living organisms integrate multiple signals from their exposome, the totality of environmental influences experienced throughout life, to adapt to complex, non-stationary environments. While organisms are thought to flexibly prioritize relevant signals depending on context, its regulatory mechanisms remain largely unknown. Laboratory studies with precisely controlled conditions fail to capture this adaptability by isolating organisms from the complex exposome. Here, we developed a machine learning framework, Inverse Signal Importance (ISI), to infer how organisms prioritize external signals from time-series data of environmental factors and physiological responses. We applied ISI to analyze gonadal development in medaka fish under natural outdoor conditions, tracking gonadosomatic index alongside environmental signals including water temperature, day length, and solar radiation over two years. Our analysis revealed that signal importance levels exhibit complex dynamics distinct from simple environmental periodicity and correlates significantly with specific gene expression patterns. Notably, genes associated with temperature-related signal importance display differential expression between outdoor and controlled laboratory conditions, suggesting their role in environmental adaptation. These findings indicate that ISI effectively captures latent physiological dynamics in adaptation of exposome. By decomposing biological responses into deterministic and adaptive components, ISI provides a novel approach to uncover mechanisms of organismal adaptation in natural environments.

bioinformatics↗

bioRxiv2024

Quantification of Cyclin-CDK dissociation constants in living cells using fluorescence cross-correlation spectroscopy with green and near-infrared fluorescent proteins.

The cell cycle is a highly coordinated process governed by cyclin-bound cyclin-dependent kinases (CDKs). While the interaction between cyclin and CDK are well-documented, the dissociation constants (Kd) between specific cyclin-CDK pairs within living cells remain poorly understood. Fluorescence cross-correlation spectroscopy (FCCS) enables the quantification of the Kd, but challenges remain in selecting an optimal pair of fluorescent molecules for FCCS in a living cell. In this study, we demonstrate that mNeonGreen and phycocyanobilin-bound miRFP670 represent a suitable pair for FCCS in living cells from the viewpoint of high photostability and low bleed-through. This fluorescent protein pair enables us to measure the Kd values of the cyclin-dependent kinase Cdc2 and B-type cyclin Cdc13 in fission yeast cells. Moreover, we conducted a comprehensive analysis of the Kd values for 36 cyclin-CDK complexes, formed by 9 distinct cyclins and 4 CDKs, in mammalian cells, including unconventional cyclin-CDK pairs. These findings provide insights into the redundancy of cyclin-CDK binding in cell cycle progression, with potential implications for understanding cell cycle regulation in both fission yeast and higher eukaryotes.

cell biology↗

bioRxiv2024

Self-organization of spermatogenic wave coordinates sustained sperm production in the mouse testis

Spermatogenesis takes place in the testis, relying on the ordered turnover of differentiating cells supplied from stem cells. Classic histological analyses have revealed that this process shows hierarchical spatiotemporal patterning known as the spermatogenic cycle, wave, and descent of segmental order, indicative of currently underexplored mechanisms of tissue- and organ-scale homeostasis. Here, using mice, we conducted high-resolution, wide-field, and ultra long-term live imaging studies in vivo and ex vivo, combined with whole-organ mapping of differentiation stages. Such trans-scale measures demonstrate how stereotypic local cell turnover is coordinated into characteristic phase waves propagating along the seminiferous tubules, further organized into organ-scale patterning over the tubule loops. Minimal mathematical modeling shows that such higher-order dynamics can emerge from the local coupling of autonomous oscillators, which are rooted in delayed feedback interplay between stem and differentiating cells via retinoic acid signaling. These findings highlight a self-organization mechanism underpinning organ-scale homeostasis and constant sperm production.

developmental biology↗

bioRxiv2024

Drp1-mediated mitochondrial fission protects macrophages from mtDNA/ZBP1-mediated sterile inflammation and inhibits post-infarct cardiac remodeling

BackgroundIschemic heart disease is a leading cause of death worldwide, and heart failure after myocardial infarction (MI) is a growing issue in this aging society. Macrophages play central roles in left ventricular (LV) remodeling after MI. Mitochondria consistently change their morphology, including fission and fusion, but the role of these mitochondrial morphological changes, especially in macrophages, is unknown. This study aims to illuminate the effects and mechanisms of Dynamin-related protein 1 (Drp1), a molecule mediating mitochondrial fission, in macrophages for cardiac remodeling after MI. MethodsThis study utilized genetically altered mice lacking Drp1 in monocytes/macrophages (Drp1-KO) to elucidate the specific role of macrophage Drp1 in post-infarct LV remodeling. ResultsDeletion of Drp1 in macrophages exacerbated LV remodeling, including reduced ejection fraction and increased LV diameters, which resulted in decreased survival after MI. Histological analysis indicated increased fibrosis and sustained macrophage accumulation in Drp1-KO mice. Blockade of Drp1 in macrophages decreased mitochondrial fission and impaired mitophagy, leading to the subsequent release of mitochondrial DNA (mtDNA) to the cytosol and induction of inflammatory cytokines. This induction was abrogated by an autophagy inducer, Tat-beclin1, or siRNA-mediated knockdown of Z-DNA Binding Protein 1 (ZBP1). Deletion of ZBP1 in bone marrow-derived cells abrogated LV remodeling induced by Drp1 inhibitor, Mdivi-1. ConclusionMacrophage Drp1 plays a critical role in the pathobiology of LV remodeling after MI, especially mitochondria quality control mechanisms. Macrophage Drp1 could be a novel therapeutic molecule to mitigate the progression of LV remodeling and consequent heart failure after MI.

biochemistry↗

bioRxiv2024

Evolutionary conserved RLF, a plant cytochrome b5-like heme-binding protein, is essential for organ development in Marchantia polymorpha

In Arabidopsis thaliana, REDUCED LATERAL ROOT FORMATION (RLF), a cytochrome b5-like heme-binding domain (Cytb5-HBD) protein, is necessary for proper lateral root formation. Whereas the other Cytb5-HBD proteins in A. thaliana regulate different metabolic reactions, RLF is unique as it specifically regulates organ development. However, it remains unknown whether heme binding to RLF is necessary for its function, and whether RLF orthologs in different plant species also regulate organ development. We demonstrate that RLF binds to heme in vitro and that the two histidine residues, which are conserved among Cytb5-HBD, are crucial for both heme binding and its biological function in A. thaliana. In addition, MpRLF, a RLF ortholog in Marchantia polymorpha, rescues the lateral root formation phenotype of the A. thaliana rlf mutant. Mprlfge, the loss-of-function mutation in the MpRLF, resulted in delayed thallus growth and inhibited both gemma cup and antheridiophore formation. Transcriptome analysis using Mprlfge revealed that MpRLF affects several metabolic pathways. Our findings indicate that MpRLF is essential for vegetative and reproductive development in M. polymorpha, suggesting that the RLF-dependent redox reaction systems are evolutionarily conserved as crucial mechanisms for organ development across diverse plant species.

plant biology↗

bioRxiv2024

Retention of DLK1 in the endoplasmic reticulum identifies roles for EGF domain-specific O-glycans in the secretory pathway

In the endoplasmic reticulum (ER), O-glycosylation by O-fucose, O-glucose, and O-GlcNAc occurs in the epidermal growth factor-like (EGF) domains of secreted or transmembrane glycoproteins. Previous studies focusing on Notch receptors have revealed the pivotal role of these O-glycans in the cell surface expression of Notch or secretion of truncated Notch fragments. Although it has been demonstrated that O-fucose, O-glucose, and O-GlcNAc stabilize individual EGF domains, their role in the secretory pathway after the completion of the folding process remains unexplored. In this study, we used delta-like 1 homolog (DLK1) containing six consecutive EGF domains as a model glycoprotein to investigate the role of EGF domain-specific O-glycans in the secretory pathway. Semi-quantitative site-specific glycoproteomics of recombinantly expressed DLK1 revealed multiple O-fucose and O-glucose modifications in addition to an unusual EOGT-dependent O-hexose modification. Consistent with the results of the secretion assay, inactivation of the glycosyltransferases modifying O-fucose and O-glucose, but not the newly identified O-hexose, perturbed the transport of DLK1 from the ER during retention using the selective hooks (RUSH) system. Importantly, the absence of O-fucose did not result in an apparent loss of O-glucose modification within the same EGF domain, and vice versa. Given that protein O-fucosyltransferase 1 and protein O-glucosyltransferase 1 activities depend on the folded state of the EGF domains, O-glycans affected DLK1 transport independently of the folding process required for O-glycosylation in the ER. These findings highlight the distinct roles of O-glycans in facilitating the transport of DLK1 from the ER to the cell surface.

biochemistry↗

bioRxiv2024

ZO-1 shuttles between tight junctions and podosomes by riding ERK activation waves during collective cell migration

Collective cell migration is essential in various physiological processes, including embryonic development, wound healing, and cancer metastasis. However, the mechanisms by which individual cells achieve coordinated movement remain elusive. Here, we demonstrate that zonula occludens-1 (ZO-1), a scaffolding protein of tight junctions (TJs), dynamically translocates to form cell-to- extracellular matrix (ECM) adhesion complexes, podosomes, at the basal cell surface during migration. The translocation of ZO-1 is regulated by extracellular signal-regulated kinase (ERK) activity and its interaction with F-actin. ZO-1 at podosomes contributes to traction force generation and cell invasion, while ZO-1 at TJs mediates intercellular propagation of ERK activation, facilitating collective cell migration. These findings elucidate the versatile roles of ZO-1 in cell adhesion and movement, providing insights into the mechanisms coordinating the discrete movements of individual cells into a cohesive and directed collective cell migration.

cell biology↗

bioRxiv2024

Ephrin Forward Signaling Controls Interspecies Cell Competition in Pluripotent Stem Cells

In the animal kingdom, evolutionarily conserved mechanisms known as cell competition eliminate unfit cells during development. Interestingly, cell competition also leads to apoptosis of donor cells upon direct contact with host cells from a different species during interspecies chimera formation. The mechanisms underlying how host animal cells recognize and transmit cell death signals to adjacent xenogeneic human cells remain incompletely understood. In this study, we developed an interspecies cell contact reporter system to dissect the mechanisms underlying competitive interactions between mouse and human pluripotent stem cells (PSCs). Through single-cell RNA-seq analyses, we discovered that Ephrin A ligands in mouse cells play a crucial role in signaling cell death to adjacent human cells that express EPHA receptors during interspecies PSC co-culture. We also demonstrated that blocking the Ephrin A-EPHA receptor interaction pharmacologically, and inhibiting Ephrin forward signaling genetically in the mouse cells, enhances the survival of human PSCs and promotes chimera formation both in vitro and in vivo. Our findings elucidate key mechanisms of interspecies PSC competition during early embryogenesis and open new avenues for generating humanized tissues or organs in animals, potentially revolutionizing regenerative medicine.

cell biology↗