Biology subjects

Yamamoto, T.

Publications and source records attributed to Yamamoto, T..

At least 19 recordsLinked to original sources

bioRxiv2026

NLGN3-tagging system for Evaluating Membrane Localization Applied to Drug Screening

Aberrant membrane localization of proteins often results in functional impairment, contributing to the development of pathological conditions. Neuroligin-3 (NLGN3) is a rare but recurrent genetic risk factor for autism spectrum disorder (ASD). Comparing surface localization across NLGN3 variants requires that surface signal be referenced to expression level in the same cell. Using NLGN3 as a model, we developed I-CLiQ, a live-cell method in which the target coding sequence is introduced at a single site of a fixed vector backbone and DsRed is co-encoded as an internal expression reference, based on a 2A peptide of Perina nuda virus modified to abolish ribosomal skipping. Combining I-CLiQ with AlphaFold/AlphaMissense analysis, we evaluated ASD-associated NLGN3 variants. Structural modeling predicted steric clashes for p.R451C, p.P514S, and p.R597W. I-CLiQ-based flow cytometry confirmed that these variants significantly decrease surface expression. Furthermore, as a proof-of-concept application, we used I-CLiQ to evaluate two compounds, 4-phenylbutyrate (4-PBA) and 3-amino-1-propanesulfonic acid (3-APS); 4-PBA partially restored the surface expression of p.R451C and p.R597W. These findings establish I-CLiQ as a quantitative tool for analyzing membrane trafficking defects and demonstrate its applicability to compound screening for variants associated with conformational diseases.

cell biology↗

bioRxiv2026

Dietary phosphorus restriction enables multigenerational breeding of α-Klotho-deficient rats

Severe -Klotho deficiency causes early mortality and reproductive impairment, limiting the maintenance and physiological analysis of rat models. We generated rats carrying a CRISPR/Cas9-mediated -Klotho deletion spanning exons 1-5 and evaluated dietary phosphorus restriction primarily in the Wistar-Imamichi background. Maternal low-phosphorus (LP) feeding from mating through lactation was associated with higher overall survival to weaning (92.6% versus 85.8% under normal-phosphorus conditions) and a higher proportion of KO animals among weaned survivors (34/113 versus 23/145). Maternal LP feeding also reduced plasma phosphorus in KO pups. Continued LP feeding after weaning supported growth, gonadal development, and natural KO x KO breeding. Across 15 litters, 74 of 85 offspring survived to weaning, and KO colonies were maintained to at least the fifth generation. We additionally characterized 24-h metabolic rhythms in LP-maintained KO animals using indirect calorimetry. These profiles remained heterogeneous under a light-dark cycle. In conclusion, dietary phosphorus restriction provides a reliable strategy for the multigenerational maintenance of severe -Klotho-deficient rats, establishing a maintainable model to investigate residual metabolic and physiological phenotypes.

physiology↗

bioRxiv2026

Spindle size scaling secures mitotic fidelity against whole-genome doubling-associated mechanical stress

Although whole-genome doubling (WGD) accompanies a drastic increase in chromosome number, post-WGD cells often continue to divide. How mitosis is sustained under increased chromosome number remains largely unknown. Here, we found that WGD cells require longer mitotic spindles than isogenic diploids to maintain spindle bipolarity. WGD increased mechanical stress on spindle poles during metaphase, associated with a higher risk of pole fragmentation. Disrupting kinetochore-microtubule attachment alleviated pole stress and fragmentation in WGD cells, suggesting that WGD-linked mechanical stress arises from spindle-chromosome interactions. Artificial spindle elongation reduced the pole stress and mitigated pole fragmentation defects in WGD cells. Our findings identify chromosome gain as a critical mechanical challenge to spindle organization and establish spindle size scaling as an adaptive mechanism that preserves mitotic fidelity after WGD.

cell biology↗

bioRxiv2026

Loss of starch synthase IIa alleviates the negative impact of high temperature on rice starch during grain filling

High temperatures during grain filling stage are becoming increasingly frequent, compromising both grain and eating quality and thereby driving demand for heat-resilient cultivars. Such conditions are known to reduce the expression of granule-bound starch synthase I (GBSSI) and starch branching enzyme IIb (BEIIb), which are involved in starch biosynthesis, resulting in a decrease in amylose content and an increase in long-chain amylopectin. Thus, the present study introduced functional mutation in starch synthase IIa (SSIIa) that increases the proportion of short amylopectin chains to genetically compensate for the high-temperature-induced increase in amylopectin long chain. Rice lines carrying the ss2a mutation were grown at two locations with cooler (Akita) and warmer (Okayama) temperatures. Their grain traits, starch structure, and eating quality were compared. The ss2a mutant lines showed an increased proportion of short amylopectin chains as well as an increased apparent amylose content. Furthermore, these alterations in starch structure varied with the grain-filling temperature of the cultivation sites, ultimately affected eating quality. These results suggest that enriching short amylopectin chain via the ss2a mutation can counteract the increase in long amylopectin chain caused by high temperatures during grain filling, thereby maintaining a desirable starch structure and eating quality.

plant biology↗

bioRxiv2026

Sensory neuron dysfunction and hyperexcitability in dorsal root ganglia at disease onset in the SOD1G93A mouse model of ALS.

Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disorder traditionally characterized by motor neuron degeneration, but emerging evidence indicates sensory system involvement. Despite reports of sensory abnormalities in some patients, the molecular and functional alterations in dorsal root ganglion (DRG) neurons remain insufficiently characterized. We investigated DRG pathology at disease onset in 12-week-old SOD1G93A mice using an integrated transcriptomic, morphological, and electrophysiological approach. RNA sequencing of lumbar DRG identified 35 differentially expressed genes, predominantly upregulated, enriched in oxidative stress-related and phagosome pathways. Comparative analysis with motor neuron transcriptomes revealed distinct gene expression profiles, indicating sensory neuron-specific molecular responses. Immunohistochemistry demonstrated reduced soma diameter in both A- and C-fiber DRG neurons. Nav channel colocalization increased for Nav1.7 in A fibers and Nav1.8 in both fiber types, whereas Nav1.6 was unchanged. Whole-cell patch-clamp recordings showed depolarized resting membrane potential, increased spike amplitude, and enhanced repetitive firing in A-fiber neurons, consistent with hyperexcitability, while C fibers showed no significant functional changes. These findings demonstrate early molecular, structural, and functional alterations in primary sensory neurons in ALS, supporting pathology beyond motor neurons and identifying sensory neuron excitability as a potential therapeutic target.

neuroscience↗

bioRxiv2026

KIFC1 overexpression induces monopolar spindles by preventing centrosome separation during rapid cleavage divisions

Bipolar spindle assembly is essential for accurate chromosome segregation. KIFC1, a conserved Ran- regulated minus-end-directed kinesin-14 motor, accumulates in the nucleus during interphase and promotes chromatin-mediated spindle assembly during mitosis and meiosis. In human oocytes, reduced KIFC1 levels destabilize meiotic spindles, a defect that can be rescued by increasing KIFC1 expression. However, how KIFC1 expression levels affect mitotic spindle stability during cleavage divisions in vertebrates remains unclear. Here, we show that whereas an approximately 50% reduction in KIFC1 causes no detectable defects in spindle assembly, approximately 10-fold overexpression of KIFC1 induces monopolar spindle formation, leading to chromosome mis-segregation and embryonic lethality in medaka early embryos. KIFC1 overexpression results in ectopic centrosomal localization during interphase, impairing the separation of duplicated centrosomes before mitotic entry. Analyses of KIFC1 mutants demonstrated that these centrosome separation defects require KIFC1s microtubule-binding and motor activities and are further enhanced by deletion of KIFC1s nuclear localization sequences. Together, our findings demonstrate that tight regulation of KIFC1 expression and its nuclear sequestration is essential for the proper separation and positioning of duplicated centrosomes before mitotic entry, thereby ensuring efficient bipolar spindle assembly during the rapid cleavage divisions of vertebrate embryos. HighlightsO_LIKIFC1 accumulates in the nucleus and at the embryonic spindle midplane via the Ran pathway. C_LIO_LIPartial KIFC1 depletion does not impair spindle assembly in medaka early embryos. C_LIO_LIKIFC1 overexpression induces monopolar spindles by preventing centrosome separation. C_LIO_LICentrosome separation defects require KIFC1 microtubule-binding and motor activity. C_LI

cell biology↗

bioRxiv2026

Regucalcin-containing extracellular vesicles suppress M2 macrophage polarization and attenuate tumor progression in vivo

Regucalcin (RGN) plays diverse roles in cell biology, highlighting its importance in both physiological and pathological conditions. Prostate cancer patients with higher RGN expression exhibited significantly longer disease-free survival. Although RGN is a cell signaling suppressor, the molecular mechanisms underlying tumor suppression by RGN in the tumor microenvironment through cell-cell communication remain unclear. PC3 prostate cancer cell lines stably expressing RGN or a control vector were generated for this study. Extracellular vesicles (EVs) were isolated from these cell lines using differential ultracentrifugation. The murine macrophage cell line J7441 was treated with isolated EVs, and effects on M2 polarization were evaluated using qRT-PCR and western blot analysis. To assess the potential anti-tumor effects of EVs, PC3 parental cells were subcutaneously implanted at two sites per mouse, followed by intratumoral injection of the respective EVs. Tumor volume was monitored. Harvested fresh frozen tumor tissues underwent immunofluorescence staining for CD206, an M2 macrophage marker. RGN was detected in EVs from RGN-expressing cells, and treatment with these RGN-containing EVs was associated with reduced tumor growth and reduced M2 macrophage polarization in vitro and in vivo. Furthermore, recombinant RGN protein reduced the levels of p-AKT1 and p-ERK1/2. Moreover, the suppression of M2 macrophage polarization by RGN-containing EVs was accompanied by decreased p-AKT1 and p-ERK1/2 in vitro. This study describes an EV-associated mechanism that may contribute to the regulation of macrophage polarization and indicates that RGN-containing EVs merit further evaluation as a candidate approach for cancer treatment. Causal validation, such as macrophage depletion or CD206 knockdown, and evaluation in additional models remain to be addressed in future studies.

cancer biology↗

bioRxiv2026

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↗

bioRxiv2026

Mutation-agnostic gene insertion therapy for RHO-associated autosomal dominant retinitis pigmentosa using zinc finger nucleases

PurposeAutosomal dominant retinitis pigmentosa caused by mutations in the rhodopsin gene (RHO-adRP) is among the most prevalent inherited retinal dystrophies. With nearly 100 distinct pathogenic variants identified to date, the mutational heterogeneity of RHO-adRP severely limits the clinical utility of mutation-specific therapeutic strategies. We aimed to develop a mutation-agnostic gene insertion therapy using homology-independent targeted integration (HITI) mediated by zinc finger nuclease ZF-ND1 targeting the human RHO 5'-UTR, and to validate its preclinical efficacy, safety, proof-of-concept, and proof-of-mechanism. MethodsWe developed two AAV serotype 5 (AAV5) vectors: one encoding the ZF-ND1 pair (AAV5-ZFN) and one carrying the therapeutic donor cassette (AAV5-RHO), delivered by subretinal co-injection. ZF pairs targeting the RHO 5'-UTR were arranged and refined by in vitro validation; AAV vector optimization and mechanistic verification were performed in human induced pluripotent stem cell (hiPSC)-derived retinal organoids-derived retinal organoids; longitudinal proof-of-concept efficacy and safety were assessed in a humanized RHO-T17M rat disease model by 6-month optical coherence tomography (OCT); and proof-of-mechanism was evaluated in non-human primate retina. ResultsWe identified a ZF-ND1 pair achieving cleavage efficiency comparable to the SpCas9 RNP previously validated for HITI-mediated editing in mouse retina, and optimized the ZF array composition and NLS configuration for efficient editing especially in post-mitotic photoreceptors. HITI-mediated donor integration was confirmed across multiple cell types and ZFN:donor ratios. In the humanized rat disease model, the therapeutic vector provided outer nuclear layer (ONL) preservation by 6 months, with AAV5-ZFN:AAV5-RHO ratios of 1:1 and 1:2 maintaining ONL thickness above the preservation threshold. In the non-human primate retina, the fraction of HITI-edited rod photoreceptors exceeded the 20% therapeutic correction threshold in the successfully treated individual. ConclusionsThese findings support the advancement of this therapeutic vector to first-in-human trials as a mutation-agnostic insertion therapy applicable to all patients with RHO-adRP, irrespective of the specific causative variant.

genetics↗

bioRxiv2026

Possible function of Hox2 in atrial siphon fusion of the ascidian Ciona

The hallmark of sessile adult ascidians is a vase-like shape with a single oral and atrial siphon. Ciona, however, develops two atrial siphons after metamorphosis, which subsequently fuse into one. The mechanisms underlying this fusion are unknown. This study suggests that Hox2 controls this process. Hox2-knockout animals using Transcription-Activator-Like Effector Nuclease (TALEN) retain two atrial siphons throughout their lives. During normal fusion, epidermal cells between the siphons flatten along the anterior-posterior axis. This cellular flattening does not occur in Hox2-knockout animals, suggesting that the shape change in the epidermal cells produces tension, allowing the atrial siphon openings to converge at the midline for fusion. Hox2-knockout animals lack cupular organs, which are suspected hydrodynamic sensors in the internal epithelium of the fused atrial siphon and on the sperm duct. Among several knockout attempts, atrial siphon fusion was reproduced by only one TALEN pair, suggesting that this phenotype is driven by a mutation having a broader effect than those abolishing protein function. Many ascidians, unlike Ciona, develop a single atrial siphon shortly after metamorphosis. Our findings suggest that a phylogenetically conserved gene, Hox2, establishes this group-specific atrial siphon formation mechanism in Ciona.

developmental biology↗

bioRxiv2026

Human club cells derived from pluripotent stem cells reveal new insights into epithelial lineage plasticity through structural and functional validation

Airway epithelial homeostasis relies on multiple specialized cell types, with club cells playing central roles in maintaining epithelial integrity and regulating inflammation. Environmental insults such as allergens, viral infections, or pollutants preferentially damage club cells, impairing epithelial repair and contributing to pulmonary diseases. However, the functional properties of club cells remain incompletely defined, and tractable human models are lacking. Herein, we establish a robust platform to differentiate human pluripotent stem cells (hPSCs) into club cells exhibiting their hallmark secretory features, appropriate epithelial organization, and functional properties. Single-cell transcriptomic analyses and lineage trajectory inference revealed unexpected epithelial plasticity: hPSC-derived club cells give rise to multiciliated epithelial cells through a deuterosomal intermediate--a previously uncharacterized trajectory. Additionally, a distinct club cell subset exhibited transcriptional features indicative of neuroendocrine and goblet cell differentiation potential. This study uncovers club cell plasticity and establishes a hPSC-based platform for studying airway development, regeneration and disease modeling.

cell biology↗

bioRxiv2026

Complementary δ2-protocadherin expression delineates parallel basal ganglia circuits in primates

The basal ganglia (BG) form anatomically and functionally segregated yet integrative parallel circuits, but the molecular mechanisms specifying them remain unclear. We immunohistochemically mapped the expression of three {delta}2-protocadherin ({delta}2-PCDH) cell adhesion molecules--PCDH10, PCDH17, and PCDH19--in the BG of macaques. Within the striatum, each PCDH exhibited regional gradients of expression along the rostro-caudal and ventromedial-dorsolateral axes. The three PCDHs showed complementary distributions that continuously delineated molecular boundaries corresponding to functional subdivisions in a graded fashion. Such complementary distributions were also observed in the BG output nuclei. Given that neurons expressing the same {delta}2-PCDH in distinct BG structures preferentially connect with each other, the three {delta}2-PCDH expression patterns could define functional territories within parallel BG circuits. Together, the complementary expression of PCDH10, PCDH17, and PCDH19 broadly align with the distinct BG circuits, respectively, suggesting molecular codes underlying the segregated yet integrative parallel organization of the primate BG.

neuroscience↗

bioRxiv2026

Changes in the microbiome of the trophosome of Lamellibrachia satsuma induced by rearing

BackgroundAdult vestimentiferan tubeworms inhabiting hydrothermal vents and cold seeps lack a mouth and anus and rely entirely on organic matter produced by sulfur -oxidizing autotrophic bacterial symbionts in their trophosomes. These symbionts, which predominantly belong to the genus Proteobacteria, are acquired horizontally from the environment. However, the effects of rearing conditions that differ from natural habitats on the microbiome composition or abundance of these bacteria remain unclear. MethodsWe conducted a metagenomic analysis of Lamellibrachia satsuma reared in an aquarium under sulfide-supplemented and sulfide-free conditions. ResultsImmediately after collection, the microbiome was dominated by known symbionts within {gamma}-Proteobacteria, exhibiting low species diversity. After 6 months of rearing, the abundance of these symbionts significantly decreased under both conditions, whereas overall bacterial diversity increased. In particular, -Proteobacteria became more abundant under sulfide-supplemented conditions, while {delta}-Proteobacteria predominated in the absence of sulfide. Despite these changes, symbionts were not entirely lost, and the hosts survived for 6 months, likely due to their low metabolic rate. These findings suggest that the microbiome of L. satsuma can respond flexibly to changes in the rearing environment. They also indicate that the hosts metabolism can be maintained even with a smaller quantity of symbiotic bacteria.

zoology↗

bioRxiv2026

Topological defects and coherent myocardial chirality shape torsional heart contraction

The efficient pumping of the mammalian heart relies on torsional contractile motion generated by its highly ordered three-dimensional (3D) architecture of myocardial fibres. However, the topological principles governing how its complex geometry translates into contractile mechanics remain elusive. Here, we show that the mammalian heart forms a chiral nematic field, a biological analogue to 3D liquid crystals, whose topological organisation underlies its function. Analysis of 3D imaging data revealed disclination lines, continuous assemblies of topological defects characteristic of nematic systems, within the compact myocardium. Finite-element simulations reveal that these defects are not mere structural irregularities but can locally modulate contractile behaviour and reduce mechanical work. In heterotaxy hearts with reversed global anatomy (situs inversus), myocardial fibres retain a predominantly counter-clockwise twist, similar to that of the normal heart, but with a small clockwise component near the base. This decoupling of tissue-level chirality from systemic left-right patterning suggests that cardiac twist is an intrinsic property of the myocardial fibre. Mechanical simulations of situs inversus heart demonstrate that the coherence of transmural chirality, rather than its specific orientation, is critical for contractile efficiency. Together, these findings establish the heart as a topological material and reveal how organised chiral fields generate robust organ-level mechanical function.

biophysics↗

bioRxiv2026

Natural variation in rice mitogen-activated protein kinase 4 contributes to increased photosynthetic rate under field conditions

Improving rice (Oryza sativa L.) yield requires a balanced enhancement of both sink size and source capacity. While many QTLs for sink size have been identified, only a few are known for source capacity, which is essential for achieving high yield. Here we identified qHP10 as a major QTL for increased photosynthetic rate by using chromosome segment substitution lines derived from a cross between the high-yielding indica cultivar Takanari and the average-yielding japonica cultivar Koshihikari. High-resolution mapping combined with CRISPR/Cas9-induced mutagenesis revealed that the causative gene underlying qHP10 is Mitogen-Activated Protein Kinase 4 (OsMPK4). A near-isogenic line carrying the OsMPK4Takanari allele (NIL-OsMPK4) had a 15-25% higher photosynthetic rate than Koshihikari. NIL-OsMPK4 also had higher stomatal conductance than Koshihikari but similar stomatal pore size and density, indicating that increased stomatal aperture increases photosynthetic rate. This enhancement is likely attributable to the down-regulation of OsMPK4 expression, which increases stomatal conductance and thus promotes CO2 uptake. Our findings demonstrate that OsMPK4 is a promising genetic target for increasing source capacity and, potentially, rice yield through molecular breeding. (175 words)

plant biology↗

bioRxiv2026

Macrophage immunosenescence prolongs intraocular inflammation in aged mice via impaired induction of regulatory T cells

Immune-mediated intraocular inflammation, called uveitis, is a leading cause of global blindness, with the highest burden of visual impairment falling on older individuals. Immunosenescence, the functional changes in immune cells with aging, impacts the age-associated immune response, but how immunosenescence and the molecular regulators of the age-associated immune response affect the clinical course of uveitis remains unclear. In the murine model of experimental autoimmune uveitis (EAU), aged mice demonstrated a delayed onset and peak of intraocular inflammation compared to young mice. In contrast to the canonical monophasic inflammation that rapidly resolves in young mice, aged mice developed persistent, chronic inflammation. Transcriptomic and flow-cytometric analyses of immune cells and the receptor-ligand interactome revealed a dominant macrophage-CD4+ T cell signature. This signaling pathway was functionally altered on both ends: macrophages from aged mice had an impaired capacity to generate peripherally induced regulatory T cells (pTreg) through an IL-6 regulated pathway, while CD4+ T cells co-cultured with aged macrophages demonstrated increased proliferation. Our study establishes aging as a key regulator of the effector immune response in uveitis. Regulatory T cells, specifically pTreg, are essential for resolving inflammation in uveitis and an impaired ability to induce pTreg led to a sustained, chronic inflammatory uveitis phenotype in old mice, thereby linking immunosenescence to persistent neuroinflammation. These findings highlight potential therapeutic avenues for vision-threatening uveitis, especially in older patients.

immunology↗

bioRxiv2026

In vivo xenogenic reconstitution of human alveolar epithelial architecture and function

An urgent need exists for lung models that accurately replicate human physiological profiles. We developed a chimeric mouse model enabling targeted ablation of alveolar type 2 (AT2) cells and lung macrophages, creating niches for endoscopically transplanted human induced pluripotent stem cell (hiPSC)-derived lung progenitors (hLPs). These engrafted cells were retained for 24 weeks, demonstrating self-renewal and differentiation potential, surfactant protein secretion, and maintaining alveolar phosphate homeostasis, suggesting their maturation into AT2 cells. Furthermore, transplantation of hLPs derived from disease-specific hiPSCs recapitulated the phenotype of pulmonary alveolar microlithiasis. The architecture, function, and metabolism of human alveolar epithelium were accurately replicated in vivo. This model has the potential to link experimental models and first-in-human studies, facilitating the development of novel therapies for intractable lung diseases.

developmental biology↗

bioRxiv2025

Non-linear gene sets for digital biomarkers of amyotrophic lateral sclerosis

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease caused by the loss of motor neurons. Accurate and accessible blood-based diagnosis of neurodegenerative diseases, including ALS, is becoming increasingly critical. It would be of a major clinical advantage to be able to distinguish ALS based on gene expression profiles of blood cells, but this still remains to be established. We analyzed existing data of peripheral blood mononuclear cells (PBMCs) of ALS patients by machine learning, the Maximum Mean Discrepancy (MMD), minimizing the issue of multi-collinearity shown in a multiple regression model, and identified a non-linear combination of gene sets to classify healthy controls and ALS, since non-linear approaches can capture intricate gene-gene interactions and threshold effects, which are often critical for accurately distinguishing disease from healthy states. In the gene expression profiles of PBMCs, a combination of expression levels in 3 genes, PRKAR1A, QPCT, and TMEM71, enabled us to classify ALS with an area under the curve (AUC) accuracy of 0.83 from the public database, which were then confirmed by laboratory blood samples with an AUC accuracy of 0.85. Furthermore, we found the expression levels of PRKAR1A, QPCT, and TMEM71 in motor neurons derived from induced pluripotent stem cells (iPSCs), the cell type at the core of the pathology, classified ALS with an accuracy of AUC 0.79. This approach of discriminating ALS with non-linear gene combinations may be useful for identifying ALS molecular biomarkers for blood-based diagnosis as well as for arriving at a completely new perspective of ALS pathogenesis.

molecular biology↗