Biology subjects

Usui, T.

Publications and source records attributed to Usui, T..

At least 19 recordsLinked to original sources

bioRxiv2026

Stepwise bladder carcinogenesis reveals transcriptional reprogramming involving MMP1 and COL7A1

Bladder cancer develops through multistep molecular alterations, yet the events underlying tumor initiation and progression remain poorly understood. Here, we reconstructed stepwise bladder carcinogenesis using canine bladder organoids combined with chemical carcinogenesis and serial xenotransplantation. Carcinogen-exposed normal organoids generated benign tumors that subsequently progressed to invasive carcinomas. Despite a low tumor mutational burden and limited acquisition of cancer-associated mutations, malignant progression was accompanied by extensive transcriptional reprogramming, including enrichment of epithelial-to-mesenchymal transition programs. COL7A1 and MMP1 were progressively upregulated during progression, and knockdown of either gene suppressed organoid proliferation and invasion. These functional dependencies were reproduced in independently established spontaneous canine bladder cancer organoids, where silencing of either gene also reduced xenograft growth and mitosis-related gene programs. MMP1 knockdown decreased COL7A1 expression, suggesting a potential regulatory relationship. MMP1 was also elevated in basal/squamous human bladder cancers, and its depletion suppressed human bladder cancer cell proliferation. These findings identify transcriptional reprogramming and MMP1/COL7A1 dependencies as prominent features of malignant progression.

cancer biology↗

bioRxiv2026

The membrane-tethered cis-ligand Belly roll elicits GPCR signaling thereby enabling adaptive avoidance behaviors

Animals adapt their behavioral responses to sensory stimuli through neuromodulatory circuits. Increasing fluid osmolality drives water-seeking behaviors via neuromodulation. However, the neural circuits and molecular mechanisms linking internal osmotic state to behavioral adaptation remain unclear. Here, we show that desiccation stress increases hemolymph osmolality and enhances avoidance of dry substrates in Drosophila larvae, enabling larvae to seek humid environments. We identify the abdominal leucokinin-producing (ABLK) neurons as a key circuit node that mediates this adaptive response. We further show that the GPI-anchored protein Belly roll (Bero), a member of the lymphocyte antigen-6/urokinase-type plasminogen activator receptor (LU) superfamily, acts as a non-canonical endogenous cis-ligand for the neuropeptide G protein-coupled receptor Allatostatin C receptor 2 (AstC-R2). Genetic, biochemical, and imaging analyses revealed that Bero activates AstC-R2 to induce phospholipase C {beta} (PLC{beta})-dependent signaling, thereby suppressing sensory transmission in ABLK neurons. Desiccation-induced increase in hemolymph osmolality activates VMA-AstC neurons to trigger Allatostatin C (AstC) release, which antagonizes Bero-mediated AstC-R2 signaling and promotes dry substrate avoidance. Together, our findings uncover a neural circuit and a molecular mechanism by which changes in internal physiological state dynamically switch GPCR signaling through the opposing actions of membrane-tethered and secreted ligands, thereby reshaping adaptive behavioral responses.

neuroscience↗

bioRxiv2026

Continuous Nuclear Export of p62/SQSTM1 Is Essential for Kidney Homeostasis

The selective autophagy receptor p62/SQSTM1 dynamically shuttles between the nucleus and cytoplasm through distinct nuclear localization and export signals, yet the physiological significance of this trafficking has remained unknown. Here, we generated mice carrying a deletion of the p62 nuclear export signal (dNES) to determine the in vivo role of p62 nuclear export. Homozygous dNES mice developed progressive podocyte injury, glomerulosclerosis, and fatal renal failure by 6-7 weeks of age, whereas heterozygous and dNES/- mice did not develop renal dysfunction. Loss of nuclear export caused constitutive nuclear accumulation of p62, accompanied by the formation of insoluble ubiquitin-positive aggregates and widespread alterations in the renal proteome, including activation of energy metabolism-related pathways and suppression of developmental programs. We previously demonstrated that the lipid peroxidation product 4-hydroxy-2-nonenal (4-HNE) inhibits the nuclear export receptor XPO1, resulting in nuclear retention of p62 in cultured cells. The present findings provide in vivo evidence that continuous nuclear export of p62 is indispensable for maintaining kidney homeostasis and reveal that excessive nuclear accumulation, rather than cytoplasmic depletion, underlies p62-mediated toxicity. Collectively, these findings establish continuous nuclear export of p62 as an essential mechanism for maintaining kidney homeostasis. Significance StatementThe adaptor protein p62/SQSTM1 continuously shuttles between the nucleus and cytoplasm, but the physiological significance of this trafficking has remained unknown. Here, we show that disrupting the nuclear export signal of p62 causes progressive podocyte injury, glomerulosclerosis, and fatal kidney failure through excessive nuclear accumulation and aggregate formation. In contrast, dNES/+ and dNES/- mice remain healthy, demonstrating that excessive nuclear accumulation, rather than cytoplasmic depletion, drives disease. These findings identify continuous nuclear export as a fundamental mechanism that prevents toxic nuclear accumulation of p62 and preserves kidney homeostasis.

cell biology↗

bioRxiv2026

Eco-evolutionary dynamics are shaped by competition in experimental range expansions

Most theory and empirical research on range expansion assumes populations spread into empty landscapes with abundant resources, however expanding populations are likely to compete with residents. In mathematical models, interspecific competition can lead to pushed wave dynamics, where expansions are driven mainly by individuals dispersing from the core, leading to steeper wavefronts and increased genetic diversity at the edge. These predictions are yet to be tested empirically, and the role of interspecific competition in mediating evolution during range expansion is unclear. We used an experimental system with two duckweed species to ask if interspecific competition leads to pushed-like dynamics and to assess how competition alters evolution during range expansion. We found that competition with a resident reduced expansion speed and absolute variance among replicate expansions, suggesting competition makes expansion speed more predictable. Interspecific competition also changed the relative frequencies of genotypes at the leading edge. While competition was associated with some features of pushed waves, genotype diversity did not vary between treatments. Our results demonstrate that demographic and evolutionary patterns associated with pushed waves may not be universal, and that incorporating selective pressures into future research on eco-evolutionary dynamics of range expansion is key to understanding spreading populations in nature.

ecology↗

bioRxiv2026

A practical pipeline for volume rendering of trillion-voxel tomographic data

Recent advancements in tomography produce imaging data of geological materials (rocks and fossils) at trillion-voxel scales with multi-channels. Such high-resolution datasets are potentially keys to unveil evolutionary biological information with various shapes and sizes that have not been ever discovered. Volume rendering is an ideal visualization approach for them because it treats all voxels without relying on user-defined surface boundaries. However, these large-scale real-world tomographic data have rarely been volume-rendered at their native resolution, limiting the examination of rich morphological information. Here, we demonstrate a de facto standard volume-rendering pipeline running on a graphical processing unit (GPU)-equipped supercomputing system toward multi-channel, trillion-voxel tomographic data. Our workflow preserves original resolution, capturing detailed morphological information spanning microscopic to macroscopic scales. Systematic comparison of node types shows that GPU memory, rather than host memory, is the primary bottleneck. Our results establish a baseline for large-scale, multi-channel volume rendering of real tomographic data and demonstrate its applicability to geological samples. This work is presented as a practical demonstration of large-scale volume visualization.

paleontology↗

bioRxiv2026

Niche differentiation confers coexistence prior to the species boundary in an aquatic plant

Despite the prevailing view that ecological divergence drives speciation, we know little about when or how nascent lineages evolve the ecological differences needed to coexist upon secondary contact. Here, we apply ecological coexistence theory to quantify the potential for coexistence among 126 allopatric lineages of the globally distributed duckweed Spirodela polyrhiza. Using competition experiments simulating secondary contact, we found that rapid accumulation of niche differences stabilized coexistence to permit sympatry among potentially interbreeding lineages. Competition against sister-species Spirodela intermedia further showed that niche differences accumulate more slowly post-speciation, revealing that niche differences enabling coexistence evolve well before timescales at which speciation is complete. Our findings suggest that rapid coexistence may thus contribute to time-lags in speciation, shaping both the origin and maintenance of biodiversity.

ecology↗

bioRxiv2026

A GPI-anchored Ly6/uPAR superfamily gene belly roll is expressed in multiple peptidergic neurons in Drosophila melanogaster larvae

The Lymphocyte antigen-6 (Ly6)/urokinase-type plasminogen activator receptor (uPAR) superfamily (LU super family) of proteins are involved in diverse biological processes. In Drosophila melanogaster, members of the LU superfamily have undergone lineage-specific gene duplication and acquired specialized functions in distinct tissues. A glycosylphosphatidylinositol (GPI)-anchored LU family protein Belly roll (Bero) has recently been shown to regulate larval escape behavior; however, its cellular expression profile and potential roles remain incompletely understood. In this study, we generated a bero-GAL4T2A transgenic line to delineate endogenous bero expression. This analysis revealed that bero is expressed in the peptidergic neurons in the central nervous system (CNS) that had not been documented in previous studies, as well as in the peripheral nervous system (PNS) and non-neuronal tissues, such as the anal pad and epidermis. Reanalysis of publicly available single-cell RNA sequencing (scRNA-seq) datasets demonstrated that bero is expressed in several peptidergic neurons. These findings suggest that Bero is specifically expressed in diverse peptidergic neurons and may play important roles in coordinating hormonal and neural regulation in D. melanogaster.

neuroscience↗

bioRxiv2025

Roles of a Drosophila ADAM 10 transmembrane metalloprotease, Kuzbanian, in tissue architecture and function of the adult adipose tissue

Various molecular mechanisms in mature adipose tissue regulate whole-body physiology. In contrast, our current understanding of the development of this tissue is limited. The adult fat body (AFB) of Drosophila melanogaster is an emerging model for investigating the regulatory mechanisms of adipose tissue morphogenesis in vivo. AFB precursor cells undergo long-range directional and collective migration, proliferation, and homotypic adhesion, leading to the formation of monolayered AFB during metamorphosis. Here, we show that a Drosophila ADAM10 transmembrane metalloprotease, Kuzbanian (Kuz), is required for the AFB morphogenesis in the precursor cells at the onset of adhesion. Histological and ultrastructural analyses revealed that the kuz knocked-down AFB cells formed multilayered structures or clumps, indicating that Kuz is essential for forming a single-cell-thick tissue sheet. Furthermore, adults with the morphologically altered AFB were supersensitive to starvation stress. Finally, we tested the hypothesis that Notch (N), a well-characterized substrate for Kuz or ADAM10, participates in AFB development, and found that knocking down N reduced AFB area coverage and made the adults less adaptive to starvation, similar to kuz knockdown. Altogether, our study highlights the critical role of Kuz in both the architecture and function of adult adipose tissue.

developmental biology↗

bioRxiv2025

For colonization success, should hosts and microbes travel alone, together, or swap partners along the way?

Understanding what determines colonization success is a key challenge of global change ecology. Microbiomes that enhance host performance are likely to be co-introduced with hosts during colonization due to their intimate association. Yet, it is unclear how co-introduced microbes will impact host colonization, as both the microbiome and its effects could vary upon introduction into a new habitat. Here, we used duckweeds --a cosmopolitan, freshwater angiosperm-- and their microbiome to track colonization dynamics during an experimental co-introduction in the wild. Notably, we found that host performance was substantially reduced when plants were co-introduced with microbes non-local to the introduced habitat, relative to hosts with a local microbiome. Moreover, negative impacts from the non-local microbiome persisted for multiple host generations despite a rapid turnover in microbiome composition during colonization. Overall, we suggest that considering the co-introduced microbiome can help predict host colonization success under global change.

ecology↗

bioRxiv2024

Competition enables rapid adaptation to a warming range edge

Most predictions of how climate warming will affect species ranges ignore species interactions. We tested experimentally if range-edge populations can adapt to warming within competitive communities. Using a model plant species, we found that adaptation to warming range edges was possible only when populations evolved with interspecific competitors. Moreover, competitors enabled the evolution of both high-temperature tolerance (CTmax) and increased thermal performance breadth at the range edge. Yet, competitors limited adaptation at the range core and had no detectable effects on population growth rates at the range edge, suggesting that responses to competition and warming can be cryptic. Our results highlight the urgency of including community context in predicting future range shifts, showing that antagonistic interactions do not necessarily hinder adaptation to climate deterioration.

ecology↗

bioRxiv2023

Refinement of a technique for collecting and evaluating the osmolality of haemolymph from Drosophila larvae

ex vivo physiological experiments using small insect models such as Drosophila larvae have become increasingly useful to address fundamental biological questions. To perform such experiments, various artificial saline solutions have been developed, but their osmolality varies significantly from one to the next. Such a variation of osmolality stems, in part, from the difficulty of determining the true value of haemolymph osmolality in Drosophila larvae. Thus, there is a pressing need to refine protocols for collecting and measuring the osmolality of the larval haemolymph. Two major obstacles are thought to impede the accurate analysis of haemolymph collected from small insects: melanin formation and gut-derived contamination. Here, we greatly refined existing haemolymph collecting methods, evaluated the purity of the collected haemolymph under melanin-free conditions, and concluded that the true value of haemolymph osmolality is close to 306.0 mOsm kg-1 in Drosophila larvae.

physiology↗

bioRxiv2023

Temperature-dependence and genetic variation in resource acquisition strategies in a model freshwater plant

O_LIUnderstanding how competition varies with environmental stress is critical to anticipating species and community responses to rapid environmental change. While the stress-gradient hypothesis predicts the strength of competition to decrease with increasing stress, our understanding of how competition varies with stress is limited by a lack of mechanistic understanding of how resource-use traits underlying competitive dynamics respond to stress. C_LIO_LIHere, we use duckweeds in the Lemna species complex to measure how phenotypic and genetic variation in R* (a resource acquisition trait representing the minimum resource requirement for positive population growth) varies with high-temperature stress to better understand how stress alters competitive ability for essential resources. C_LIO_LIWe found that heat stress increased the R* of Lemna plants for nitrogen acquisition. Because lower R* values predict dominance in competitive dynamics where resources are limiting, this indicates that under stressful, high temperatures, plants could experience increased sensitivity to competition due to the higher resources required to sustain positive population growth rates. C_LIO_LIWe found minimal genetic variation in R* across 11 local genotypes within the Lemna species complex, indicating that selection on resource acquisition strategies for essential resources such as nitrogen may be constrained in nature. The expression of genetic variation in R* for nitrogen was further reduced under heat stress, suggesting that the response to selection for R* could be particularly constrained under high-temperature stress. C_LIO_LIContrary to predictions drawn from the gleaner-opportunist trade-off, we did not find evidence for a trade-off in resource acquisition strategies under benign conditions or high-temperature stress. Plants with lower R* (i.e., higher growth rates under lower nitrogen levels) were not constrained to have lower growth rates under higher nitrogen levels, possibly because the chosen genotypes have not diverged across resource acquisition strategies or because Lemna spp. has escaped this constraint. C_LIO_LIImportantly, our work outlines that high-temperature stress could increase sensitivity to competition through increased requirement for resources while reducing the evolutionary potential for Lemna species to respond to selection for resource traits. This study acts as a key step to understanding the mechanistic traits behind competitive dynamics in resource-limited and stressful environments. C_LI

ecology↗

bioRxiv2023

Range expansion is both slower and less predictable across a spatial gradient in temperature

Rapid evolution in colonizing populations can alter our ability to predict future range expansions. Recent theory suggests that the dynamics of replicate range expansions are less variable, and hence more predictable, with increased selection at the expanding range front. Here, we test whether selection from environmental gradients across space produces more consistent range expansion speeds, using the experimental evolution of replicate duckweed populations colonizing landscapes with and without a temperature gradient. We found that range expansion across a temperature gradient was slower on average, with range-front populations displaying higher population densities, and genetic signatures and trait changes consistent with directional selection. Despite this, we found that with a spatial gradient range expansion speed became more variable and less consistent among replicates over time. Our results therefore challenge current theory, highlighting that chance can still shape the genetic response to selection to influence our ability to predict range expansion speeds.

ecology↗

bioRxiv2022

The GPI-anchored Ly6 protein Belly roll regulates Drosophila melanogaster escape behaviors by modulating the excitability of nociceptive peptidergic interneurons

Appropriate modulation of escape behaviors in response to potentially damaging stimuli is essential for survival. Although nociceptive circuitry has been studied, it is poorly understood how genetic contexts affect the relevant escape responses. Using an unbiased genome-wide association analysis, we identified a Ly6/-neurotoxin family protein, Belly roll (Bero), which negatively regulates Drosophila nociceptive escape behavior. We show that Bero is expressed in abdominal leucokinin-producing neurons (ABLK neurons) and bero knockdown in ABLK neurons resulted in enhanced escape behavior. Furthermore, we demonstrated that ABLK neurons responded to the activation of nociceptors and initiated the behavior. Notably, bero knockdown reduced the persistent neuronal activity and increased the evoked nociceptive responses in ABLK neurons. Our findings reveal that Bero modulates an escape response by regulating distinct neuronal activities in ABLK neurons.

neuroscience↗

bioRxiv2022

Inter-organ Wingless/Ror/Akt signaling regulates nutrient-dependent hyperarborization of somatosensory neurons

Nutrition in early life has profound effects on an organism, altering processes such as organogenesis. However, little is known about how specific nutrients affect neuronal development. Dendrites of class IV neurons in Drosophila larvae become more complex when the larvae are reared on a low-yeast diet compared to a high-yeast diet. Our systematic search for key nutrients revealed that the neurons increase their dendrite densities in response to a combined deficiency in vitamins, metal ions, and cholesterol. These nutrients affect dendrite branching through the Wingless/Ror/Akt pathway between the neuron and closely located muscles, and this short range-pathway is regulated by a systemic Upd2-Stat92E pathway between the fat body and muscles. Additionally, the low-yeast diet blunts neuronal light responsiveness and light avoidance behavior, which may help larvae optimize their survival strategies under low-nutritional conditions. Together, our studies illustrate how the availability of specific nutrients affects neuronal development through inter-organ signaling.

developmental biology↗

bioRxiv2021

Pan-cancer organoid validation of tumor outlier chromosomal amplification events

Somatic copy number gains are pervasive in many cancer types, yet their roles in oncogenesis are often poorly explored. This lack of understanding is in part due to broad extensions of copy gains across cancer genomes spanning large chromosomal regions, obscuring causal driver loci. Here we employed a multi-tissue pan-organoid modeling approach to validate candidate oncogenic loci identified within pan-cancer TCGA data by the overlap of extreme copy number amplifications with extreme expression dysregulation for each gene. The candidate outlier loci nominated by this integrative computational analysis were functionally validated by infecting cancer type-specific barcoded full length cDNA lentiviral libraries into cognate minimally transformed human and mouse organoids bearing initial oncogenic mutations from esophagus, oral cavity, colon, stomach, pancreas and lung. Presumptive amplification oncogenes were identified by barcode enrichment as a proxy for increased proliferation. Iterative analysis validated DYRK2 at 12q15, encoding a serine-threonine kinase, as an amplified head and neck squamous carcinoma oncogene in p53-/- oral mucosal organoids. Similarly, FGF3, amplified at 11q13 in 41% of esophageal squamous carcinomas, was validated in p53-/- esophageal organoids in vitro and in vivo with pharmacologic inhibition by small molecule and soluble receptor FGFR antagonists. Our studies establish the feasibility of pan-organoid contextual modeling of pan-cancer candidate genomic drivers, enabling oncogene discovery and preclinical therapeutic modeling.

cancer biology↗

bioRxiv2020

Embrace heterogeneity to improve reproducibility: A perspective from meta-analysis of variation in preclinical research

The reproducibility of research results has been a cause of increasing concern to the scientific community. The long-held belief that experimental standardization begets reproducibility has also been recently challenged, with the observation that the reduction of variability within studies can lead to idiosyncratic, lab-specific results that are irreproducible. An alternative approach is to, instead, deliberately introduce heterogeneity; known as "heterogenization" of experimental design. Here, we explore a novel perspective in the heterogenization program in a meta-analysis of variability in observed phenotypic outcomes in both control and experimental animal models of ischaemic stroke. First, by quantifying inter-individual variability across control groups we illustrate that the samount of heterogeneity in disease-state (infarct volume) differs according to methodological approach, for example, in disease-induction methods and disease models. We argue that such methods may improve reproducibility by creating diverse and representative distribution of baseline disease-state in the reference group, against which treatment efficacy is assessed. Second, we illustrate how meta-analysis can be used to simultaneously assess efficacy and stability (i.e., mean effect and among-individual variability). We identify treatments that have efficacy and are generalizable to the population level (i.e. low inter-individual variability), as well as those where there is high inter-individual variability in response; for these latter treatments translation to a clinical setting may require nuance. We argue that by embracing rather than seeking to minimise variability in phenotypic outcomes, we can motivate the shift towards heterogenization and improve both the reproducibility and generalizability of preclinical research.

neuroscience↗

bioRxiv2020

Expansion dynamics and marginal climates drive adaptation across geographic ranges

Every species experiences limits to its geographic distribution. Some evolutionary models predict that populations at range edges are less well-adapted to their local environments due to drift, expansion load, or swamping gene flow from the range interior. Alternatively, populations near range edges might be uniquely adapted to marginal environments. In this study, we use a database of transplant studies that quantify performance at broad geographic scales to test how local adaptation, site quality, and population quality change from spatial and climatic range centers towards edges. We find that populations from poleward edges perform relatively poorly, both on average across all sites (15% lower population quality) and when compared to other populations at home (31% relative fitness disadvantage), consistent with these populations harboring high genetic load. Populations from equatorial edges also perform poorly on average (18% lower population quality) but, in contrast, outperform foreign populations (16% relative fitness advantage), suggesting that populations from equatorial edges have strongly adapted to unique environments. Finally, we find that populations from sites that are thermally extreme relative to the species niche demonstrate strong local adaptation, regardless of their geographic position. Our findings indicate that both nonadaptive processes and adaptive evolution contribute to variation in adaptation across species ranges.

evolutionary biology↗