Biology subjects

Nishimura, T.

Publications and source records attributed to Nishimura, T..

At least 19 recordsLinked to original sources

bioRxiv2026

Diverse signaling proteins recruit RCC1-Like Domain proteins to the plasma membrane through a common structural framework.

Plants translate diverse environmental cues into spatially regulated growth responses through intracellular signaling mechanisms that remain incompletely understood. Here, we identify the BREVIS RADIX (BRX) domain of RCC1-LIKE DOMAIN (RLD) proteins as a versatile interaction module that recognizes multiple signaling proteins in Arabidopsis. We identified members of the PHYTOCHROME KINASE SUBSTRATE (PKS) and BIG GRAIN (BG) families as novel RLD interactors families, in addition to the previously characterized LAZY1-LIKE (LZY) proteins and BREAKING OF ASYMMETRY IN THE STOMATAL LINEAGE (BASL). Structural, biochemical, and cell-based analyses demonstrate that these diverse partners, despite having divergent interaction sequences, bind a common surface on the RLD BRX domain to recruit RLD to the plasma membrane. This interaction relies on a shared {beta}-strand-based recognition mode, in which distinct peptide conformations accommodate binding to the same BRX-domain surface. Furthermore, we show that RLD2 and RLD3 contribute to hypocotyl phototropism, and that disrupting the conserved PKS interaction motif abolishes PKS4 function in this response. Together, our findings identify the RLD BRX domain as a molecular platform for diverse protein interactions and establish a PKS-RLD module that operates in phototropism. Furthermore, these findings strongly suggest that RLD recruitment to the plasma membrane via PKS underlies phototropic signal transduction.

plant biology↗

bioRxiv2026

TorPause: Efficient Static Organ Preservation for Transplants

Transplantation is limited by how long organs survive outside the body. Existing preservation methods slow metabolism or sustain physiological support, but neither eliminates ischemia-reperfusion injury (IRI), which shortens storage and drives organ discard. Embryonic diapause and hibernation show that mammalian cells retain a latent capacity for reversible metabolic arrest. Screening the PI3K-mTOR axis, we identified a dual inhibitor that pauses embryonic stem cells reversibly at ambient oxygen and holds intact mouse embryos in arrest for 11 days. Combined with a mitochondria-targeted hydrogen sulfide donor, this yields TorPause: a two-component flush pairing metabolic pausing with mitochondrial protection, compatible with existing preservation protocols. In a rat liver transplantation model, TorPause reduced structural injury and improved recipient survival after severe warm ischemic storage, potentially expanding the usable donor pool.

developmental biology↗

bioRxiv2026

A map of RBP-miRNA regulatory connections for deciphering the mechanisms of transcriptome remodeling in cancer

Micro-RNAs (miRNAs) are key post-transcriptional regulators of gene expression that influence cancer progression and outcome. Whereas transcriptional dysregulation of miRNA abundance underlies abnormal functionality of some miRNAs in cancer, emerging data points to RNA-binding proteins (RBPs) as prominent post-transcriptional regulators of miRNA activity. Here, by modelling the regulon activities of well-characterized miRNA families in RNA-seq data of a comprehensive collection of RBP inhibition experiments, human cell lines and tissues, we report a map of regulatory connections between 34 RBPs and 28 miRNAs. Furthermore, through a global analysis of the abundance as well as the activity of miRNAs in thousands of tumor and control samples from 17 human cancers, we show that RBP-driven regulation of miRNA activity is common in tumors and contributes to the heterogeneity in miRNA activity profiles. We uncover a set of RBPs that regulate the activity of tumor-suppressor and oncogenic miRNAs, including miR-29-3p, miR-17-5p and miR-19-3p. Of particular interest, we describe a pan-cancer negative regulatory role for DDX55 on the activity of the miR-29-3p family, a critical miRNA family with tumor suppressor functions that is involved in most human cancers. Our functional studies confirm that DDX55 inhibition restores the gene-silencing activity of miR-29-3p and reduces cancer cell viability. Overall, our study provides the first pan-cancer investigation of functional regulatory connections between RBPs and miRNAs, and highlights RBPs whose interventional modulation may serve as a new approach to reprogram abnormal miRNA activities in cancer.

genomics↗

bioRxiv2026

Calcium-independent biosensors for multiplexed in vivo imaging of extracellular lactate dynamics

Extracellular L-lactate reports cellular metabolism, but resolving its dynamics alongside intracellular metabolism and neuronal activity remains challenging. Here we develop eLACCO3 and R-eLACCO3, green and red cell-surface lactate biosensors with Ca2+-independent responses and faster response and recovery kinetics in cultured cells. Selected variants provide larger fluorescence responses than their predecessors in brain cells, slices, and living mice and improve detection of glucose-evoked extracellular lactate oscillations. Combining R-eLACCO3 with GCaMP6f enabled imaging of extracellular L-lactate simultaneously with odor-evoked activity in anesthetized mice and cortical activity in awake mice. These biosensors enable multiplexed measurements of extracellular lactate dynamics in relation to intracellular metabolism and neuronal activity.

molecular biology↗

bioRxiv2026

Stromal CTHRC1 protects the valvular interstitium from macrophage-associated inflammatory remodeling and calcification

Background: Calcific aortic valve disease (CAVD) is characterized by progressive inflammatory and fibrocalcific remodeling. Although valvular interstitial cells (VICs) are generally considered to drive fibrosis and osteogenic remodeling, whether injury-activated VICs mount endogenous protective responses that preserve the valvular interstitial microenvironment and restrain calcification remains unknown. Methods: We performed spatial transcriptomic profiling of aortic valves in a mouse model of endothelial injury-induced CAVD to define early injury-responsive programs within the valvular interstitium. The cellular origin and spatial distribution of candidate protective factors were examined by immunohistochemistry and lineage tracing, and their relevance to human disease was assessed using stenotic aortic valves. The functional role of CTHRC1 was investigated using genetic Cthrc1 deficiency combined with longitudinal hemodynamic assessment, histological analysis, and spatial transcriptomic profiling. Results: Spatial transcriptomics identified Cthrc1 as a prominent component of an early injury-induced stromal response in the expanding valvular interstitium. CTHRC1 was strongly expressed in activated VICs within thickened murine valve leaflets and human stenotic aortic valves. Lineage tracing demonstrated that the expanded VIC population arose predominantly from PDGFR{beta}+ resident interstitial cells, with minimal endothelial contribution. Despite comparable early hemodynamic responses to endothelial injury, Cthrc1 deficiency exacerbated chronic valvular calcification. Spatial profiling of Cthrc1-deficient valves revealed pronounced interstitial accumulation of galectin-3+ foamy macrophages, accompanied by mitochondrial respiratory-chain signature loss and cell death-associated pathway activation. These findings indicate that transient CTHRC1 induction after endothelial injury defines an endogenous stromal protective response that preserves the valvular interstitial microenvironment and limits macrophage-associated tissue injury and subsequent dystrophic calcification. Conclusions: Injury-activated VICs are not merely effectors of pathological remodeling, but can engage an endogenous tissue-protective response through CTHRC1. These findings identify a previously unrecognized stromal defense mechanism linking endothelial injury to macrophage-associated inflammatory remodeling and dystrophic calcification and suggest CTHRC1-dependent stromal protection as a potential therapeutic axis for limiting CAVD progression.

molecular biology↗

bioRxiv2026

Lysyl oxidase drives ccRCC progression by coordinating HIF-2α transcription program with tumor microenvironment

Clear cell renal cell carcinoma (ccRCC) is driven by persistent HIF-2 transcription program initiated by VHL loss, yet molecular mediators sustaining this program are poorly defined. Using single-cell transcriptomics, we identified lysyl oxidase (LOX) as a driver of ccRCC progression, selectively enriched in a hypoxia/epithelial-mesenchymal transition (EMT) gene program associated with poor outcome. While LOX oxidizes and stabilizes HIF-2 by antagonizing HUWE1-mediated ubiquitination and degradation, thereby sustaining HIF-2-driven transcription in cancer cells, it also remodels extracellular matrix (ECM) and promotes angiogenesis in the tumor microenvironment (TME). Genetic or pharmacological inhibition of LOX destabilizes HIF-2, disrupts ECM, inhibits angiogenesis, and suppresses tumor initiation, growth, and metastasis in vivo. LOX inhibition enhances anti-angiogenic therapy response and remains effective in belzutifan-resistant HIF-2 G323E-mutant tumors. Nuclear LOX protein correlates with nuclear HIF-2 in high-grade patient tumors. Together, LOX coordinates HIF-2 transcription program with TME and is a therapeutic target in ccRCC.

cancer biology↗

bioRxiv2026

Mitochondrial one-carbon enzyme MTHFD1L sustains stemness and metastatic progression in breast cancer

One-carbon (1C) metabolism is frequently upregulated in cancer to support anabolic growth and nucleotide biosynthesis. However, the contribution of mitochondrial 1C metabolism to cancer stemness and metastatic progression remains incompletely understood. Here, we identify methylenetetrahydrofolate dehydrogenase 1-like (MTHFD1L), a mitochondrial 1C metabolic enzyme, as a critical regulator of breast cancer stemness, tumor initiation, and lung metastasis. Genetic depletion of MTHFD1L in triple-negative breast cancer (TNBC) cell lines and patient-derived breast cancer models markedly impaired proliferation, sphere formation, tumorigenicity, and lung colonization. Metabolomic profiling revealed extensive metabolic rewiring following MTHFD1L loss, characterized by accumulation of the purine biosynthetic intermediates SAICAR and AICAR together with perturbations in glycolytic and pentose phosphate pathways. Importantly, suppression of lung metastasis was accompanied by reduced expression of the stemness-associated transcription factor SOX2 and decreased proliferative activity in metastatic lesions. Collectively, our findings establish MTHFD1L as a key metabolic dependency linking mitochondrial 1C metabolism to stem-like properties and metastatic progression in breast cancer, and highlight MTHFD1L as a promising therapeutic target in metastatic TNBC.

Cancer Biology↗

bioRxiv2026

Coordinated Membrane Deformation Driven by a Minimal Set of Spiroplasma MreB Isoforms

Spiroplasma are wall-less helical bacteria that swim by switching the handedness of their helices. In most bacteria, MreB, a bacterial actin, forms relatively static filaments beneath the membrane to organize cell wall synthesis. In contrast, Spiroplasma eriocheiris encodes five MreB isoforms (SpeMreBs), and swimming requires a pair of isoforms, SpeMreB5 together with SpeMreB4 (or the related isoform SpeMreB1) (1) Yet how these MreBs generate force and membrane deformation remains unclear. To examine the membrane-deforming activities of SpeMreBs, we demonstrated a simple reconstitution system using the non-motile synthetic bacterium JCVI-syn3B and purified SpeMreBs expressed in Escherichia coli. Lysates of syn3B expressing SpeMreB5 deformed liposomes in a concentration-dependent manner. In contrast, lysates co-expressing both SpeMreB5 and SpeMreB4 showed a plateau in the frequency of deformation, suggesting that SpeMreB4 suppresses membrane deformation driven by SpeMreB5. Deformed liposomes exhibited either fluctuating or stable behaviors. ATP depletion changed both the frequency and behavior of deformation, indicating that membrane remodeling depends on the nucleotide state of SpeMreBs. Reconstitution with purified SpeMreBs from E. coli confirmed that SpeMreB5 alone deforms membranes, whereas SpeMreB1, a member of the same class as SpeMreB4, suppresses deformation. These results suggest that membrane shape in Spiroplasma is dynamically regulated by antagonistic interactions among isoforms of SpeMreBs isoforms and their nucleotide-dependent assembly states.

synthetic biology↗

bioRxiv2026

Rab32/Rab38-positive Lysosome-Related Organelle degrades lipid droplet in hepatocytes by microautophagy

Rab32 and Rab38 are paralogous small GTPases involved in the biogenesis of lysosome-related organelles (LROs), yet their roles in hepatic lipid metabolism remain poorly defined. Here, Rab32 and Rab38 double-knockout (DKO) male mice exhibited an age-dependent increase in body weight accompanied by hepatic lipid accumulation, suggesting impaired hepatic lipid processing. In AML12 hepatocytes, Rab32 and Rab38 localized to ring-like, LAMP1-positive structures characteristic of LROs, whose size increased with cell confluence. Pharmacological inhibition of lysosomal acid lipase with orlistat led to the accumulation of lipid droplets (LDs) within Rab32/38-positive LROs, indicating that LD degradation occurs in these compartments. Additional treatment with bafilomycin A1 revealed invagination-like internal membrane structures within enlarged LROs. These processes were not affected by artificial inhibition of macroautophagy, highlighting the involvement of microautophagy. Ring-like signals positive for phosphatidylinositol 3-phosphate (PI3P) or phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2) were detected within or adjacent to LRO membranes, and LDs were frequently associated with these structures, suggesting a role for PI3P and PI(3,5)P2 in internal membrane formation. Vps4B was also required for efficient LD incorporation. Consistently, Rab32/38 double-knockdown (DKD) AML12 cells exhibited increased lipid accumulation, indicating impaired LD engulfment. Together, these findings identify Rab32/38-positive LROs as a structural platform for microautophagy-mediated lipid droplet degradation in hepatocytes.

cell biology↗

bioRxiv2025

Microbiome-host interactions drive a trade-off between sleep quality and lifespan in Drosophila

Understanding the interactions between various aging processes and the resulting heterogeneity in aging is crucial for promoting healthy aging. Here, we provide evidence that heterogeneity in microbiome and host interactions contributes to diversifying aging phenotypes in sleep, gut integrity, and longevity in Drosophila. Aged flies exhibiting sleep fragmentation preserve gut integrity, accompanied by a shift in microbiota composition, particularly an increase in Acinetobacter junii. A. junii induces sleep fragmentation via its metabolite, urocanic acid, through serotonin receptor-dependent dopamine upregulation. In parallel, A. junii exploits the host response to promote its growth, leading to lifespan extension, which is recapitulated by genetically modified Escherichia coli, suggesting a trade-off between sleep quality and lifespan. Our study demonstrates a systematic mechanism underlying aging heterogeneity, suggesting interventions through bacterial supplements.

animal behavior and cognition↗

bioRxiv2025

OddSNP: a predictive framework for optimizing multiplexed single-cell RNA-seq experiments

Donor multiplexing is a powerful strategy to increase scale, lower the costs, and reduce batch effects in single-cell RNA sequencing (scRNAseq), but clear guidelines for experimental design are lacking, forcing researchers to risk costly demultiplexing failures. To address this, we introduce SNP-Information Content (SNP-IC), a quantitative metric computable from simple unpooled pilot data that accurately predicts the success of genotype-based demultiplexing. Across multiple large-scale datasets using stem cell and organoid models, we establish a robust SNP-IC threshold of approximately 50, above which cells can be reliably assigned to their donor of origin. For more challenging genotype-free approaches, we define a pairwise metric, cpSNP-IC, and demonstrate a much higher requirement of approximately 3,000. Our open-source framework, oddSNP, implements this predictive model, allowing researchers to perform in silico titrations of sequencing depth and donor complexity to optimize experimental design before committing to large-scale studies. oddSNP provides a practical framework, enabling researchers to strategically optimize sequencing depth and donor numbers to maximize experimental success while managing costs and minimizing the risk of catastrophic data loss.

bioinformatics↗

bioRxiv2025

Genome-wide association study shows developmental robustness control by intestinal maltase via internal environment in Drosophila

Organisms encounter disturbances during development because of genetic variations, environmental shifts, and stochastic noise. However, developmental robustness and canalization buffer these fluctuations to maintain normal development. Nevertheless, understanding the underlying mechanisms that govern this robustness is challenging because of the complex interactions between these factors. In Drosophila, the number of scutellar sensory organs (SSO; macrochaetes) derived from the sensory organ precursors (SOPs) in the larval wing disc has been used as a model to study developmental robustness. Although the number of SOPs is strictly regulated by a network of signaling and transcription factors in the imaginal disc, non-intrinsic broader factors such as temperature and energy metabolism additionally influence SSO-number fluctuation. Moreover, the precise molecular mechanisms regulating the systemic control of bristle number remain unknown. In this study, we identify factors controlling bristle robustness by performing genome-wide association studies (GWAS). We observed significant single-nucleotide polymorphisms (SNPs) in the Maltase gene cluster and found that the knockdown of Maltase genes affected SSO numbers. Furthermore, Maltase-A1(Mal-A1) in the gut regulated insulin signaling systemically, thereby affecting SSO-number fluctuation. These results suggest that Mal-A1 contributes to robustness by modulating glucose availability and Drosophila insulin-like peptide 3 (dilp3) level, which affects the SOPs in a nonautonomous manner. This study presents the molecular basis of nutritional regulation of developmental robustness and highlights Maltase as a key mediator.

developmental biology↗

bioRxiv2025

Low temperature abolishes human cellular circadian rhythm through Hopf bifurcation

Circadian clocks orchestrate behavior, physiology, and metabolism in harmony with the Earths 24-h cycle. Low temperatures are known to disrupt circadian clocks in plants and poikilotherms; however, their effects on human circadian rhythms remain poorly understood. Here, we demon-strate that cold exposure abolishes the circadian rhythm in cultured human cells through diminishing the oscillation amplitude, which was restored upon rewarming. In addition, the oscillation amplitude of the 24-h temperature cycles was enhanced through resonance, reflecting the intrinsic frequency of the circadian clock. From a theoretical perspective, these dynamics correspond to Hopf bifurcation, which is confirmed by a mathematical model for the mammalian circadian clock. In contrast, the circadian amplitude of human hair follicle cells was resistant to temperature changes, indicating robust temperature homeostasis. These findings suggest that Hopf bifurcation in the circadian clock for temperature regulation is shared by homeothermic and poik-ilothermic species.

systems biology↗

bioRxiv2025

Glucagon dysfunction in the liver induces hyperplasia of PP cells and the production of glucagon and pancreatic polypeptide double-positive cells

Understanding the mechanisms that regulate cellular identity and proliferation is crucial for elucidating cellular functions. Under normal conditions, pancreatic endocrine cells express only a single hormone, and their numbers are tightly regulated. Contrary to this general principle, our study revealed a significant increase in glucagon (GCG) and pancreatic polypeptide (PP) double-positive cells (GCG+ PP+ double-positive cells), along with hyperplasia of both PP and cells in proglucagon-deficient mice. Similarly, systemic glucagon receptor-deficient mice exhibited PP-cell hyperplasia and an increase in GCG+ PP+ double-positive cells, with enhanced PP-cell self-replication observed at 4 weeks and the appearance of GCG+ PP+ double-positive cells at 10 weeks. Liver-specific glucagon receptor-deficient mice induced similar effects, which were linked to hyperaminoacidemia. Elevated glutamine levels were found to promote GCG+ PP+ double-positive cell formation via mTOR signaling, suggesting a molecular mechanism driving pancreatic endocrine cell plasticity. Collectively, these findings indicate that increased plasma amino acid levels caused by impaired glucagon action in the liver promotes the proliferation of cells and PP cells, and disturbs their cellular identity maintenance.

cell biology↗

bioRxiv2025

Development of iPSC-Derived T Cells Targeting EGFR Neoantigens in Non-Small Cell Lung Cancer

A long-sought goal of cancer immunotherapy is to mass-produce T cells that specifically target tumor neoantigens. One decisive challenge is the identification of neoantigens derived from cancer driver genes. Here, we identify T cells that recognize the NSCLC-associated EGFR C797S mutation, which confers resistance to current inhibitors and is linked to poor prognosis. To overcome limitations in T cell availability, we reprogrammed EGFR C797S-specific T cells into induced pluripotent stem cells (iPSCs) and re-differentiated them into CD8 T cells. These iPSC-derived T cells specifically recognized the EGFR C797S mutation and effectively killed cancer cells expressing this mutation. Our findings underscore the potential of targeting driver mutation-derived neoantigens for immunotherapy and demonstrate that iPSC-derived T cells can mediate antitumor effects. Collectively, this approach combining neoantigen identification with T cell reprogramming may offer a promising strategy for targeting drug-resistant tumors.

immunology↗

bioRxiv2024

Meioc-Piwil1 complexes regulate rRNA transcription for differentiation of spermatogonial stem cells

Ribosome biogenesis is vital for sustaining stem cell properties, yet its regulatory mechanisms are obscure. Herein, we show unique properties of zebrafish meioc mutants in which spermatogonial stem cells (SSCs) do not differentiate or upregulate rRNAs. Meioc colocalized with Piwil1 in perinuclear germ granules, but Meioc depletion resulted in Piwil1 accumulation in nucleoli. Nucleolar Piwil1 interacted with 45S pre-rRNA. piwil1+/-spermatogonia with reduced Piwil1 upregulated rRNAs, and piwil1+/-;meioc-/- spermatogonia recovered differentiation later than those in meioc-/-. Further, Piwil1 interacted with Setdb1 and HP1, and meioc-/- spermatogonia exhibited high levels of H3K9me3 and methylated CpG in the 45S-rDNA region. These results indicate that zebrafish SSCs maintain low levels of rRNA transcription with repressive marks similar to Drosophila piRNA targets of RNA polymerase II, and that Meioc has a unique function on preventing localization of Piwil1 in nucleoli to upregulate rRNA transcripts and to promote SSC differentiation.

developmental biology↗

bioRxiv2024

Differential clearance rate of proteins encoded on a self-amplifying mRNA vaccine in muscle and lymph nodes

ARCT-154, a recently approved self-amplifying mRNA (saRNA) vaccine, has been shown in clinical trials to induce higher levels of neutralizing antibodies and sustain them for a longer time than the conventional mRNA vaccine BNT162b2. However, the scientific evidence explaining this superiority remain elusive. Hence, we explored the temporal changes in spike protein and replicase components following a single dose of ARCT-154 vaccination in mice. The encoded spike protein reached its highest level approximately 3 days after vaccination and quickly disappeared from the rectus femoris muscle, the injection site. Although the spike protein levels also peaked at an early time point in the lymph nodes, it remained detectable 28 days after the vaccination and then disappeared by 44 days after the vaccination. Expression of nsP1, nsP2 and nsP4 was observed in the injected muscle and/or the lymph nodes for up to 15 days post-vaccination. These data suggest that prolonged expression of spike proteins in lymph nodes may, if not entirely, be responsible for the induction of higher and prolonged levels of neutralizing antibodies by the saRNA vaccine.

molecular biology↗

bioRxiv2024

Microbiome diversity, intra-mucosal bacteria and immune integration within normal and asthmatic airway mucosa

Asthma is characterized by reduced bronchial bacterial diversity and airway mucosal disruption. We examined spatial distributions of microbial sequences and host mucosal transcripts in bronchial biopsies from healthy controls and adult asthmatics. Bacteria were discovered by 16S ribosomal RNA staining in the lamina propria of all biopsies, with counts positively associated to lumenal bacterial diversity. Weighted correlation network analysis identified fifteen co-expression networks, including distinct programs of adaptive and innate immunity in differing spatial distributions. Stromal bacterial counts correlated significantly with eight of the network eigenvectors in directions compatible with beneficial relationships. The results suggest that dysbiosis may affect mucosal immunity through impaired interactions beneath the epithelial border. Intra-mucosal companion bacteria may be a potential substrate for selective management of immunity in a wide range of diseases. One-Sentence SummaryThe lung microbiome extends within the airway mucosa and associates spatially and functionally with immune networks.

microbiology↗