Biology subjects

Wada, A.

Publications and source records attributed to Wada, A..

5 recordsLinked to original sources

bioRxiv2026

Core genome MLST reveals genetic and BafA-associated phenotypic diversities in Bartonella henselae strains

Bartonella henselae is a zoonotic pathogen associated with cat-scratch disease. Although multilocus sequence typing (MLST) has been used for strain classification, its resolution for distinguishing between B. henselae isolates remains limited. We herein developed a B. henselae-specific core genome MLST (cgMLST) scheme based on whole-genome sequencing data and examined the genetic and phenotypic diversities of 80 strains derived from cats, humans, mongooses, and masked palm civets. Using the conventional MLST scheme, the 80 strains were classified into nine sequence types (STs), while cgMLST subdivided them into 72 cgSTs, demonstrating a marked improvement in discriminatory power. The cgMLST scheme comprised 1,183 core genes and showed high applicability across the 80 strains. A phylogenetic analysis revealed that ST1, which has been associated with cat-scratch disease, was further subdivided into three major clusters and two singletons, indicating high genetic heterogeneity within this ST. We also found that the bafA subtypes clustered in a manner that was largely consistent with the cgMLST-based phylogenetic structure, suggesting a close relationship between bafA variations and the genomic background of B. henselae strains. In a human umbilical vein endothelial cell proliferation assay, strains belonging to distinct cgSTs exhibited strain-dependent differences in proliferative capacity, which were associated with the bafA subtype classification. Some strains induced focal cell fragmentation and a reduced cell density at a high multiplicity of infection, indicating strain-dependent differences in endothelial cell injury. Collectively, the present results establish a high-resolution cgMLST framework for B. henselae and demonstrate that genetically distinct strains have diverse endothelial cell phenotypes.

microbiology↗

bioRxiv2026

Quantitative Framework for Assessing Mesenchymal Stem Cell Quality Driven by Poised Enhancer Decommissioning

Mesenchymal stem cell (MSC) heterogeneity and conventional phenotypic criteria limitations represent major bottlenecks in therapeutic manufacturing. Here, we present a framework to prospectively identify naturally superior MSCs by shifting from superficial markers to the digital quantification of fundamental epigenetic flaws in inferior clones. We show that intrinsic MSC functional decline is driven by targeted hypermethylation of poised enhancers, causing paradoxical derepression of developmental genes. We term this process poised enhancer decommissioning (PEnD). By isolating this universal decay axis from donor-specific immunological variability, we translate this complex epigenetic state into a streamlined transcriptomic signature: the Poised Enhancer-related Gene Expression (PErGE) score. Overcoming the limitations of standard in vitro differentiation assays, our approach enables accurate, donor-independent prediction of long-term proliferative potential. Together, our findings establish a mechanism-based biomarker of cellular aging, and provide a readily applicable tool to improve the quality control of next-generation MSC-based therapies.

cell biology↗

bioRxiv2025

Gamete release in Ciona robusta: roles of gonadotropin-releasing hormone and the photoreception system

Gamete release, an essential event for animals, is regulated by various factors including environmental stimuli, neural circuit, and endocrine molecules. In this study, we investigated the mechanisms regulating gamete release in the ascidian Ciona robusta, part of the sister group of vertebrates. Ciona is a hermaphrodite, releasing sperm first from orange-pigmented organ (OPO) at the end of the spermiduct, followed by eggs from the oviduct beneath the spermiduct knob-like structure. In this study, behavioral and morphological analyses revealed that this sequential release occurs because the knob-like structure compresses the oviduct opening at the onset of gamete release. Observations of transgenic Ciona expressing Kaede under the gonadotropin-releasing hormone 2 (Gnrh2) promoter showed that Gnrh2-expressing neurons and fibers accumulate in the epithelium around the spermiduct openings. In contrast, Gnrh1-expressing neurons are localized in the cerebral ganglion and project toward the ovary, suggesting distinct roles of GnRH1 and GnRH2 in reproductive regulation. RNA-seq and real-time PCR analyses revealed that Opsin2, Opsin3, beta-carotene-15,15-monooxygenase (Bco), and several ion channel genes are specifically expressed in the OPO, along with Gnrh2. In situ hybridization showed that these genes are localized in the innermost OPO layer, suggesting that the OPO functions as a photoreceptive organ. Although, Gnrh2 expression has been considered low in adult Ciona, our study revealed strong OPO-specific expression with photoreceptive genes. Collectively, these findings suggest that GnRH2 plays a central role in gamete release regulation, potentially in coordination with the photoreceptive system, while GnRH1 may regulate ovarian functions. These results indicate that C. robusta employs distinct GnRH systems in a tissue-specific manner to regulate reproduction.

evolutionary biology↗

bioRxiv2022

PTH regulates osteogenesis and suppresses adipogenesis through Zfp 467 in a feed-forward, cyclic AMP-dependent manner

Conditional deletion of the PTH1R in mesenchymal progenitors reduces osteoblast differentiation, enhances marrow adipogenesis and increases zinc finger protein 467 (Zfp467) expression. In contrast, genetic loss of Zfp467 increased Pth1r expression and shifts mesenchymal progenitor cell fate towards osteogenesis and higher bone mass. In this study we hypothesized that PTH1R and ZFP467 could constitute a feedback loop that facilitates PTH-induced osteogenesis and that conditional deletion of Zfp467 in osteogenic precursors would lead to high bone mass. We report that PrrxCre Zfp467 but not AdipoCre Zfp467 mice exhibit an identical phenotype to the Zfp467-/-mice with high bone mass and greater osteogenic differentiation We also found that PTH suppressed Zfp467 expression primarily via the cyclic AMP/PKA pathway. Not surprisingly, PKA activation inhibited the expression of Zfp467 and gene silencing of Pth1r caused an increase in Zfp467 mRNA transcription. Dual fluorescence reporter assays and confocal immunofluorescence demonstrated that genetic deletion of Zfp467 resulted in higher nuclear translocation of p50 that binds to the P2 promoter of the Pth1r and increased its transcription. As expected, Zfp467-/- cells had enhanced production of cyclic AMP and increased glycolysis in response to exogenous PTH. Additionally, the osteogenic response to PTH was also enhanced in Zfp467 -/-calvarial osteoblasts, and the pro-osteogenic effect of Zfp467 deletion was blocked by gene silencing of Pth1r or a PKA inhibitor. In conclusion, our findings suggest that loss or PTH1R-mediated repression of Zfp467 results in a pathway that increases Pth1r transcription via p50 and thus cellular responsiveness to PTH, ultimately leading to enhanced bone formation.

cell biology↗

bioRxiv2021

Comparative analysis of transcriptomic profiles among ascidians, zebrafish, and mice: insights from tissue-specific gene expression

Tissue/organ-specific genes (TSGs) are important not only for understanding organ development and function, but also for investigating the evolutionary lineages of organs in animals. Here, we investigate the TSGs of 9 adult tissues of an ascidian, Ciona intestinalis Type A (Ciona robusta), which lies in the important position of being the sister group of vertebrates. RNA-seq and qRT-PCR identified the Ciona TSGs in each tissue, and BLAST searches identified their homologs in zebrafish and mice. Tissue distributions of the vertebrate homologs were analyzed and clustered using public RNA-seq data for 12 zebrafish and 30 mouse tissues. Among the vertebrate homologs of the Ciona TSGs in the neural complex, 48% and 63% showed high expression in the zebrafish and mouse brain, respectively, suggesting that the central nervous system is evolutionarily conserved in chordates. In contrast, vertebrate homologs of Ciona TSGs in the ovary, pharynx, and intestine were not consistently highly expressed in the corresponding tissues of vertebrates, suggesting that these organs have evolved in Ciona-specific lineages. Intriguingly, more TSG homologs of the Ciona stomach were highly expressed in the vertebrate liver (17-29%) and intestine (22-33%) than in the mouse stomach (5%). Expression profiles for these gene suggest that the biological roles of the Ciona stomach are distinct from those of their vertebrate counterparts. Collectively, Ciona tissues were categorized into 3 groups: i) high similarity to the corresponding vertebrate tissues (neural complex and heart), ii) low similarity to the corresponding vertebrate tissues (ovary, pharynx, and intestine), and iii) low similarity to the corresponding vertebrate tissues, but high similarity to other vertebrate tissues (stomach, endostyle, and siphons). The present study provides transcriptomic catalogs of adult ascidian tissues and significant insights into the evolutionary lineages of the brain, heart, and digestive tract of chordates.

evolutionary biology↗