Biology subjects

Takada, T.

Publications and source records attributed to Takada, T..

9 recordsLinked to original sources

bioRxiv2026

Cardiomyocyte-derived Wnt5a drives doxorubicin-induced cardiomyopathy by amplifying cellular senescence

Doxorubicin (DOX) is an effective anthracycline chemotherapeutic agent, but its use is limited by cardiotoxicity that can progress to cardiomyopathy and heart failure. Cellular senescence contributes to DOX-induced cardiac injury, yet the upstream signals that initiate and propagate senescence in the injured heart remain unclear. Here, we identify Wnt5a, a non-canonical Wnt ligand, as a mediator of anthracycline cardiomyopathy. WNT5A was increased in serum from cancer patients receiving anthracycline therapy and in a pathologic human cardiomyocyte population in the context of DOX-induced cardiomyopathy. In mouse hearts, DOX induced early cardiomyocyte-enriched Wnt5a expression before overt cardiac dysfunction. Cardiomyocyte-specific Wnt5a deletion attenuated DOX-induced cardiac dysfunction, fibrosis and senescence marker induction, whereas recombinant Wnt5a and cardiomyocyte-targeted Wnt5a overexpression were sufficient to promote cardiomyocyte senescence and cardiac dysfunction. Mechanistically, DOX activated a Wnt5a-Fzd2 feed-forward axis that amplified Wnt5a expression in cardiomyocytes and propagated senescence to neighboring fibroblasts. Genetic disruption of this pathway in cardiomyocytes, fibroblasts or senescent cells reduced DOX-induced cardiomyopathy. Pharmacological inhibition of Wnt5a signaling with secreted frizzled-related protein 5 suppressed DOX-induced cardiac injury without compromising the anticancer efficacy of DOX. These findings identify Wnt5a-Fzd2 signaling as a senescence-amplifying mechanism in anthracycline cardiomyopathy and suggest a therapeutic strategy to mitigate DOX cardiotoxicity.

cell biology↗

bioRxiv2025

Population genomic scan of endogenous retrovirus insertions revealed cryptic drivers of selective sweep in wild house mouse genomes

Endogenous retroviruses (ERVs) represent a major source of structural variation in mammalian genomes, yet their diversity in wild populations remains poorly understood. Here, we conduct a comprehensive genome-wide survey of non-reference ERV insertions in wild house mice (Mus musculus) to characterize their distribution and evolutionary dynamics. Using a newly developed bioinformatics pipeline, we detected and annotated over 100,000 non-reference ERV insertions from short-read sequencing data across 163 wild mouse genomes. Our analyses revealed marked differences in ERV insertion patterns among subspecies and populations, including variation in genomic localization and population-specific polymorphisms. These heterogeneous patterns suggest distinct evolutionary histories and host-retrovirus interactions across populations. For instance, we describe the distribution of the ERV-derived Fv4 locus, which shows subspecies-restricted occurrence and confers resistance to murine leukemia viruses (MLVs). Several lines of evidence showed that the spread of Fv4 insertions in Korean population has been driven by adaptive introgression from neighboring populations. Our study provides the first large-scale population genomic scan of ERV diversity in wild house mice. By cataloguing extensive polymorphism in non-reference ERV insertions, our results highlight the role of ERVs as dynamic genomic elements that contribute to structural variation and adaptive evolution. Article SummaryEndogenous retroviruses (ERVs) are viral sequences embedded in animal genomes that can create structural genetic variation. In this study, we conducted a genome-wide survey of non-reference ERV insertions in 163 wild house mice using short-read sequencing data and a newly developed computational pipeline. We identified more than 100,000 polymorphic ERV insertions and found substantial differences among subspecies and geographic populations. One example, the ERV-derived Fv4 locus, illustrates how ERV variation can influence the genetic pattern of polymorphisms in the species. These results demonstrate that ERVs are dynamic genomic elements that contribute to population divergence and adaptive evolution.

evolutionary biology↗

bioRxiv2023

Inference of Selective Force on House Mice Genomes during Secondary Contact in East Asia

The house mouse (Mus musculus), commensal to humans, has spread globally via human activities, leading to secondary contact between genetically divergent subspecies. This pattern of genetic admixture can provide insights into the selective forces at play in this well-studied model organism. Our analysis of 163 house mouse genomes, with a particular focus on East Asia, revealed substantial admixture between the subspecies castaneus and musculus, particularly in Japan and southern China. We revealed, despite the admixture, all Y chromosomes in the East Asian samples belonged to the musculus-type haplogroup, potentially explained by genomic conflict under sex ratio distortion due to varying copy numbers of ampliconic genes on sex chromosomes. We also investigated the influence of selection on the post-hybridization of the subspecies castaneus and musculus in Japan. Even though the genetic background of most Japanese samples closely resembles the subspecies musculus, certain genomic regions overrepresented the castaneus-like genetic components, particularly in immune-related genes. Furthermore, a large genomic block containing a vomeronasal/olfactory receptor gene cluster predominantly harbored castaneus-type haplotypes in the Japanese samples, highlighting the crucial role of olfaction-based recognition in shaping hybrid genomes.

evolutionary biology↗

bioRxiv2023

Interstage flow matrices: population statistic derived from matrix population models

O_LIMany population statistics describe the characteristics of populations within and among species. These are useful for describing population dynamics, understanding how environmental factors alter demographic patterns, testing hypotheses related to the evolution of life history characteristics, and informing the effective management of populations. C_LIO_LIIn this study, we propose a population statistic: the interstage flow. The interstage flow is defined as the product of the element in the ith row, the jth column of the population projection matrix, and the jth element of the normalized stable stage distribution. C_LIO_LIThe sum of the interstage flow matrix elements is equal to the population growth rate, which is the dominant eigenvalue of the population projection matrix. The interstage flow matrix elements allow decomposition of population growth rate into component contributions made by transitions between developmental stages. C_LIO_LIWe demonstrate the utility of interstage flow matrices using matrix population models from the COMPADRE plant matrix database. We compared interstage flows among four life history/functional groups (semelparous herbs, iteroparous herbs, shrubs, and trees) and described how population growth rate reflected individual transitions related to stasis, fecundity, and growth. We found that the individual flows are different among functional groups. C_LIO_LISynthesis: The proposed population statistic, the interstage flow matrix, describes the contribution of individual developmental stage transitions to the population growth rate. The flow of individuals between developmental stages differs in distinctive ways among different life histories and functional groups. The interstage flow matrix is a valuable statistic for describing these differences. C_LI

ecology↗

bioRxiv2022

Which life history strategy can maintain high genetic diversity in plants?

Classifying a variety of plant life histories is an important step to understand ecological and evolutionary background of life history diversification in plants. Principal component analysis (PCA) of life history traits, as well as elasticity analysis using a ternary diagram, successfully categorized the diverse life histories and clarified their link to various ecological characteristics, such as population dynamics, functional traits, and conservation status. However, the relationships with population genetic properties, including genetic diversity, have not been explored very much. In this study, we overlaid annual change rate of expected heterozygosity{eta} on life history spectrum obtained by PCA and elasticity analysis to examine which life history strategy can maintain high genetic diversity over time. We found that{eta} gradually changed along the fast-slow continuum and that slow-paced life histories maintained high genetic diversity, probably due to generation overlap. Elasticity analysis showed that life histories that highly depend on stasis also maintained genetic diversity. As genetic diversity reflects adaptive potential to environmental changes, our study provides a new genetic perspective on adaptative evolution and population viability to life history study.

ecology↗

bioRxiv2021

Potential effects of life history on demographic genetic structure in stage-structured plant populations

O_LIPredicting temporal dynamics of genetic diversity is important for assessing long-term population persistence. In stage-structured populations, especially in perennial plant species, genetic diversity is often compared among life history stages, such as seedlings, juveniles, and flowerings, using neutral genetic markers. Because individuals in mature stages will die and be replaced by those in more immature stages over the course of time, the comparison among stages (sometimes referred to as demographic genetic structure) has been regarded as a proxy of potential genetic changes that accompany the turnover of constituent individuals. However, because demographic genetic structure had not been theoretically examined, the basic property and the validity of demographic genetic structure remained unclear. C_LIO_LIWe developed a matrix model which was made up of difference equations of expected heterozygosity, a common proxy of genetic diversity, of each life history stage at a neutral locus in stage-structured plant populations. Based on the model, we formulated demographic genetic structure as well as the annual change rate of expected heterozygosity (denoted as{eta} ). We obtained theoretical expectation of demographic genetic structure and{eta} from our model and compared them with computational results of stochastic simulation for randomly generated 3,000 life histories for model validation. We then examined the relationships of demographic genetic structure with effective population size Ne, which is the determinants of diversity loss per generation time, as well as with{eta} . C_LIO_LITheoretical expectations on{eta} and demographic genetic structure fitted well to the results of stochastic simulation, supporting the validity of our model. Demographic genetic structure varied independently of Ne and{eta} , while having a strong correlation with stable stage distribution: expected heterozygosity was lower in stages with fewer individuals. C_LIO_LIOur results indicate that demographic genetic structure strongly reflects stable stage distribution, rather than temporal genetic dynamics, and that inferring future genetic diversity solely from demographic genetic structure would be misleading. Instead of demographic genetic structure, the newly-defined statistics{eta} will be an useful tool to predict genetic diversity at the same time scale as population dynamics, facilitating evaluation on population viability from a genetic point of view. C_LI

genetics↗

bioRxiv2021

Insights into Mus musculus subspecies population structure across Eurasia revealed by whole-genome sequence analysis

For more than 100 years, house mice (Mus musculus) have been used as a key animal model in biomedical research. House mice are genetically diverse, yet their genetic background at the global level has not been fully understood. Previous studies suggested that they originated in South Asia and diverged into three major subspecies almost simultaneously, approximately 350,000-500,000 years ago; however, they have spread across the world with the migration of modern humans in prehistoric and historic times ([~]10,000 years ago to present), and undergone secondary contact, which have complicated the genetic landscape of wild house mice. In this study, we sequenced the whole genomes of 98 wild house mice collected from Eurasia, particularly East Asia, Southeast Asia, and South Asia. We found that although wild house mice consist of three major genetic groups corresponding to the three major subspecies, individuals representing admixture between subspecies are much more ubiquitous than previously recognized. Furthermore, several samples showed an incongruent pattern of genealogies between mitochondrial and autosomal genomes. Using samples likely retaining the original genetic components of subspecies with least admixture, we estimated the pattern and timing of divergence among the subspecies. The results are important for understanding the genetic diversity of wild mice on a global level and the information will be particularly useful in future biomedical and evolutionary studies using laboratory mice established from these wild mice.

genomics↗

bioRxiv2017

A mannitol/sorbitol receptor stimulates dietary intake in Tribolium castaneum

Perception of chemical stimuli by insects aids in accepting or rejecting food. Gustatory receptors (Grs) regulating external signals in chemosensory organs have been found in many insects. Tribolium castaneum, a major pest of stored products, possesses over 200 Gr genes. An expanded repertoire of Gr genes appears to be required for diet recognition in generalist feeders; however, it remains unclear whether T. castaneum recognizes a suite of chemicals common to many products or whether it is attracted to specific chemicals, and whether its Grs are involved in its feeding behavior. It is difficult to determine the food preference of T. castaneum based on its dietary intake due to a lack of appropriate methodology. This study established a novel dietary intake estimation method using gypsum, designated the TribUTE (Tribolium Urges To Eat) assay. T. castaneum adults were fed gypsum block without added organic compounds. Sugar preference was determined by adding sweeteners and measuring the amount of gypsum in the excreta. Mannitol was the strongest attractant of T. castaneum dietary intake; in addition, TcGr20 was responsible for mannitol and sorbitol responses in Xenopus oocyte expression, but did not respond to any other non-volatile compounds tested. The EC50 values of TcGr20 for mannitol and sorbitol were 72.6 mM and 90.6 mM, respectively, suggesting that TcGr20 is a feasible receptor for the recognition of mannitol in lower concentrations. TcGr20 was expressed in the antennae, where the perception of mannitol would occur. We examined whether TcGr20 was involved in mannitol recognition using RNAi and the TribUTE assay. The amounts of excreta in TcGr20 dsRNA-injected adults decreased significantly despite the presence of mannitol, compared to that of the control adults. Taken together, our results suggest that T. castaneum adults recognized mannitol/sorbitol using TcGr20 receptors, thereby facilitating their dietary intake.\n\nAbbreviation

biochemistry↗

bioRxiv2017

High-Resolution Maps of Mouse Reference Populations

Genetic reference panels are widely used to map complex, quantitative traits in model organisms. We have generated new high-resolution genetic maps of 259 mouse inbred strains from recombinant inbred strain panels (C57BL/6J x DBA/2J, ILS/IbgTejJ x ISS/IbgTejJ, C57BL/6J x A/J) and chromosome substitution strain panels (C57BL/6J-Chr# , C57BL/6J-Chr# , C57BL/6JChr# ). We genotyped all samples using the Affymetrix Mouse Diversity Array with an average inter-marker spacing of 4.3kb. The new genetic maps provide increased precision in the localization of recombination breakpoints compared to the previous maps. Although the strains were presumed to be fully inbred, we found residual heterozygosity in 40% of individual mice from five of the six panels. We also identified de novo deletions and duplications, in homozygous or heterozygous state, ranging in size from 21kb to 8.4Mb. Almost two-thirds (46 out of 76) of these deletions overlap exons of protein coding genes and may have phenotypic consequences. Twenty-nine putative gene conversions were identified in the chromosome substitution strains. We find that gene conversions are more likely to occur in regions where the homologous chromosomes are more similar. The raw genotyping data and genetic maps of these strain panels are available at http://churchill-lab.jax.org/website/MDA.

genetics↗