Biology subjects

Yasuda, K.

Publications and source records attributed to Yasuda, K..

13 recordsLinked to original sources

bioRxiv2026

Genomic and ecological characterization of unclassified tetraploid Echinochloa plants distributed in northern Japan

Understanding the evolutionary origins of globally noxious weeds provides insights into the genetic background of weediness. Among species of Echinochloa, the hexaploid E. crus-galli was previously thought to have arisen through hybridization and allopolyploidization between tetraploid E. oryzicola and an undiscovered diploid species, although they exhibit marked differences in both ecological and morphological characteristics. Recently, in Japan, unknown tetraploid Echinochloa plants were discovered that exhibit distinct ecological and morphological characteristics from those of E. oryzicola, with some traits showing greater similarity to those of E. crus-galli. In this study, we investigated the relationships between well-known Echinochloa species and these unknown tetraploid plants, hereafter referred to as ''ninja''. Subgenome-based read mapping analysis and phylogenetic analysis revealed that ninja possesses a distinct genomic composition, while showing close relationships to E. oryzicola in both its chloroplast and nuclear genomes. Furthermore, the identification of a very small number of ninja x E. oryzicola hybrids among field-collected individuals suggests that these two species rarely hybridize in the wild. Although ninja and E. oryzicola showed similar genomic compositions, ninja has a broader habitat range, partially overlapping with that of E. oryzicola and extending into areas occupied by E. crus-galli. Our findings indicate the possibility that hexaploid E. crus-galli may have originated from a tetraploid Echinochloa species other than E. oryzicola.

plant biology↗

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

Active Nuclear Shuttling Enables Efficient Virus-Free CAR Gene Integration Using Ready-to-Use Lipid Nanoparticles

Non-viral engineering of chimeric antigen receptor T (CAR-T) cells is highly desirable to overcome the cost, safety, and scalability limitations associated with viral vectors and electroporation. However, efficient nuclear delivery and stable genomic integration of DNA in primary human T cells remain major challenges. Here, we established a virus-free CAR-T manufacturing platform using lipid nanoparticles (LNPs) combined with a nuclear localization signal (NLS) shuttle strategy. We developed proprietary ready-to-use LNPs that enable on-demand encapsulation of nucleic acids. To overcome nuclear transport barriers, NLS-fused transposase or genome-editing nuclease was used to bind donor DNA in the cytoplasm and promote active nuclear import. This approach enabled highly efficient and low-toxicity delivery of mRNA and plasmid DNA into primary human T cells. NLS-assisted transposase delivery markedly enhanced genomic integration of the CAR gene, resulting in high expression levels and improved cell viability compared with electroporation-based methods. In addition, TRAC locus-specific targeted integration was achieved more efficiently through end-joining-based repair pathways than through homology-directed repair following LNP delivery. The resulting engineered CAR-T cells exhibited potent and antigen-specific cytotoxic activity. Together, these results demonstrate that NLS-assisted LNP delivery overcomes a key bottleneck in non-viral gene integration and provides a robust strategy for the generation of functional CAR-T cells.

bioengineering↗

bioRxiv2025

Osteochondrogenic Transdifferentiation of Vascular Smooth Muscle Cells and Microenvironmental Dynamics in Medial Arterial Calcification

BackgroundVascular calcification, particularly medial arterial calcification (MAC), considerably affects cardiovascular mortality. Current treatments are limited because of the unclear molecular mechanisms of MAC. This study aimed to establish an MAC mouse model using O-ring-induced transverse aortic constriction (OTAC) and to identify critical genes, pathways, and cellular interactions involved in MAC formation by combining lineage tracing technology and single-cell RNsA sequencing (scRNA-seq). MethodsWe developed an OTAC mouse model to mimic MAC. Adult C57BL/6J male mice underwent OTAC, and subsequent analyses were performed at various intervals. Histological and immunohistochemical evaluations were conducted to observe changes in vascular smooth muscle cells (VSMCs). Lineage tracing was used to confirm the origin of osteochondrogenic cells in the tunica media. Additionally, scRNA-seq was performed to capture the dynamic changes in VSMCs and other cell types involved in MAC development. ResultsOsteochondrogenic cells and the subsequent MAC in OTAC mice were observed using histological evaluations. Immunohistochemistry showed time-dependent decreases in -SMA expression and increases in SOX9 and RUNX2 expression in VSMCs. Lineage tracing using Myh11CreERT2;ROSA26-EGFP mice confirmed that osteochondrogenic cells originated from contractile VSMCs. scRNA-seq confirmed osteochondrogenic transdifferentiation of VSMCs and highlighted dynamic changes in surrounding cells involved in calcification-related and inflammatory processes. ConclusionThe OTAC method enabled a comprehensive understanding of the microenvironmental dynamics during MAC progression at the single-cell level. This powerful model provides a robust platform for future therapeutic intervention research. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/684711v1_ufig1.gif" ALT="Figure 1"> View larger version (58K): org.highwire.dtl.DTLVardef@c64634org.highwire.dtl.DTLVardef@12b0b9aorg.highwire.dtl.DTLVardef@106c5b4org.highwire.dtl.DTLVardef@19dd4f4_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2025

ISRIB promotes aggregation of TIA-1 by modulating its phase separation in vitro

Stress granules (SGs) are non-membranous biomolecular condensates formed through liquid-liquid phase separation (LLPS) of RNA-binding proteins (RBPs) and RNA under stress conditions. T-cell intracellular antigen-1 (TIA-1), a major RBP of SGs, can undergo LLPS via its low-complexity domain, contributing to SG nucleation. Integrated stress response inhibitor (ISRIB), a small molecule that enhances eIF2B activity and inhibits the integrated stress response, has been widely studied for its therapeutic potential in neurodegenerative diseases. However, little is known about how ISRIB directly affects the behavior of SG proteins. Here, we show that ISRIB enhances TIA-1 phase separation and promotes its aggregation in vitro. Interestingly, this effect was mitigated in the presence of RNA or cell lysates, suggesting that RNA-binding plays a protective role against ISRIB-induced aggregation. These findings imply that ISRIB alters the physical properties of SG in an RNA-dependent manner, raising important considerations for their therapeutic application. Graphic abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=56 SRC="FIGDIR/small/663586v1_ufig1.gif" ALT="Figure 1"> View larger version (14K): org.highwire.dtl.DTLVardef@7e281org.highwire.dtl.DTLVardef@1a7863eorg.highwire.dtl.DTLVardef@15e89b6org.highwire.dtl.DTLVardef@1a33ca4_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2024

Engineering of ATP synthase for enhancement of proton-to-ATP ratio

FoF1-ATP synthase (FoF1) interconverts the energy of the proton motive force (pmf) and that of ATP via mechanical rotation of the rotor complex. The H+/ATP ratio, one of the most crucial parameters in bioenergetics, varies among species due to the different number of H+-binding c-subunits, resulting in H+/ATP ratios ranging from 2.7 to 5. The present study attempted to enhance the H+/ATP ratio significantly by employing a novel approach that differs from that of nature. We engineered FoF1 to form multiple peripheral stalks, each bound to a proton-conducting a-subunit. Engineered FoF1 showed an H+/ATP ratio of 5.9, beyond the highest among naturally occurring FoF1s, enabling ATP synthesis at a low pmf, at which wild-type enzymes are unable to synthesize ATP. Structural analysis showed that the engineered FoF1 formed up to three peripheral stalks and the a-subunits. This study not only provides important insights into the H+-transport mechanism of FoF1 but also opens the possibility of engineering the foundation of cell bioenergetics.

biophysics↗

bioRxiv2023

Efficient workflow for validating homology-independent targeted integration-mediated gene insertion in rod photoreceptor cells to treat dominant-negative mutations causing retinitis pigmentosa

Among the genome-editing methods for repairing disease-causing mutations resulting in dominant inhibition, homology-independent targeted integration (HITI)-mediated gene insertion of the normal form of the causative gene is useful because it allows the development of mutation-agnostic therapeutic products. For the rapid optimization and validation of highly effective HITI-treatment gene constructs against dominant-negative inheritance of inherited retinal dystrophy, we improved the gene constructs available in both plasmid and adeno-associated virus (AAV) vectors, and established a workflow that uses in vivo electroporation to verify the in vivo efficacy. By targeting the mouse Rhodopsin gene, we derived a construct in which HITI-mediated gene insertion occurs in 80%-90% of transduced mouse rod photoreceptor cells. This construct suppressed degeneration and induced visual restoration in the mutant mice. The HITI-treatment constructs for the rhodopsin gene were shown to be effective in AAV vectors, and this construction is available for the mouse Peripherin 2 gene. These findings suggest that the workflow reported here may be useful for the generation of HITI-treatment constructs for various target genes and for the development of gene therapy products.

molecular biology↗

bioRxiv2023

Prenatal vitamin D deficiency alters immune cell proportions of young adult offspring through alteration of long-term stem cell fates

Vitamin D deficiency is a common deficiency worldwide, particularly among women of reproductive age. During pregnancy, it increases the risk of immune-related diseases in offspring later in life. However, exactly how the body remembers exposure to an adverse environment during development is poorly understood. Herein, we explore the effects of prenatal vitamin D deficiency on immune cell proportions in offspring using vitamin D deficient mice established by dietary manipulation. We found that prenatal vitamin D deficiency alters immune cell proportions in offspring by changing the transcriptional properties of genes downstream of vitamin D receptor signaling in hematopoietic stem and progenitor cells of both the fetus and adults. Our results suggest the role of cellular differentiation properties of the hematopoiesis as the long-term memories of prenatal exposure at the adult stage. Moreover, further investigations of the associations between maternal vitamin D levels and cord blood immune cell profiles from 75 healthy pregnant women and their term babies also confirm that maternal vitamin D levels in the second trimester significantly affect immune cell proportions in the babies. This highlights the importance of providing vitamin D supplementation at specific stages of pregnancy.

developmental biology↗

bioRxiv2023

Telomere-to-telomere genome assembly of an allotetraploid pernicious weed, Echinochloa phyllopogon

Echinochloa phyllopogon is an allotetraploid pernicious weed species found in rice fields worldwide that often exhibits resistance to multiple herbicides. An accurate genome sequence is essential to comprehensively understand the genetic basis underlying the traits of this species. Here, the telomere-to-telomere genome sequence of E. phyllopogon was presented. Eighteen chromosome sequences spanning 1.0 Gb were constructed using the PacBio highly-fidelity long technology. Of the 18 chromosomes, 12 sequences were entirely assembled into telomere-to-telomere and gap-free contigs, whereas the remaining six sequences were constructed at the chromosomal level with only eight gaps. The sequences were assigned to the A and B genomes with total lengths of 453 and 520 Mb, respectively. Repetitive sequences occupied 42.93% of the A genome and 48.47% of the B genome, although 32,337, and 30,889 high-confidence genes were predicted in the A and B genomes, respectively. This suggested that genome extensions and gene disruptions caused by repeated sequence accumulation often occur in the B genome before polyploidization to establish a tetraploid genome. The highly accurate and comprehensive genome sequence would contribute to elucidating the population structure of this species and could be a milestone in understanding the molecular mechanisms of the pernicious traits and to developing effective weed control strategies to avoid yield loss in rice production.

genomics↗

bioRxiv2021

Valosin-containing protein regulates the stability of amyotrophic lateral sclerosis-causing fused in sarcoma granules in cells by changing ATP concentrations inside the granules

Fused in sarcoma (FUS) undergoes liquid-liquid phase separation (LLPS) to form granules in cells, leading to pathogenic aggregations that cause neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS). Proteomics analysis revealed that FUS granules contain valosin-containing protein (VCP), a member of the AAA family ATPase. Confocal microscopy images showed that VCP co-localized in the FUS granules in cells. This study demonstrates that VCP in granules has a two-faced role in FUS granulation: VCP stabilizes de novo FUS granules, while VCP present in the granules for extended periods dissolves them. This VCP function relies on its ATPase activity to consume ATP in granules. VCP stabilizes de novo FUS by reducing intragranular ATP concentrations to a range below the cytosolic concentration. VCP continually consumes ATP during its stay in the granules, which eventually lowers ATP concentrations to a range that destabilizes the granules. VCP, therefore, acts as a timer to limit the residence of FUS granules in cells and thereby prohibits the FUS fibrillization that occurs in persistent granules. VCP ATPase activity plays a role in FUS granule turnover. Summary statementVCP recruited to FUS granules regulates the stability of the granules in a time-dependent manner by consuming intragranular ATP with its ATPase activity.

cell biology↗

bioRxiv2019

Inhibition of IRF4 in dendritic cells by PRR-independent and -dependent signals inhibit Th2 and promote Th17 responses

Cyclic AMP (cAMP) is involved in multiple biological processes. However, little is known about its role in shaping immunity. Here we show that cAMP-PKA-CREB signaling (a pattern recognition receptor [PRR]-independent) regulates conventional type-2 Dendritic Cells (cDC2s), but not cDC1s and reprograms their Th17-inducing properties via repression of IRF4 and KLF4, transcription factors (TFs) for Th2 induction. Genetic loss of IRF4 phenocopies the effects of cAMP signaling on Th17-induction, indicating that the cAMP effect is secondary to repression of IRF4. Moreover, signaling in cDC2s by a PRR-dependent microbial product, curdlan, represses IRF4 and KLF4, resulting in a pro-Th17 phenotype. These results define a novel signaling pathway by which cDC2s display plasticity and provide a new molecular basis for the novel cDC2 and cDC17 classification. In addition, the data reveal that cAMP signaling can alter DCs function and fate by repressing IRF4 and KLF4, a pathway that can be harnessed for immuno-regulation.

immunology↗

bioRxiv2019

Dual Role of Jam3b in Early Hematopoietic and Vascular Development

In order to efficiently derive hematopoietic stem cells (HSCs) from pluripotent precursors, it is crucial to understand how mesodermal cells acquire hematopoietic or endothelial identity due to their close developmental connection. Although Npas4 has been recently identified as a conserved master regulator of hemato-vascular development, the molecular mechanisms underlying the cell fate divergence between hematopoietic and vascular endothelial cells are still unclear. Here, we show in zebrafish that the divergence of hematopoietic and vascular endothelial cells in mesodermal cells is regulated by Junctional adhesion molecule 3b (Jam3b) via two independent signaling pathways. Mutation of jam3b led to the reduction of npas4l expression in the posterior lateral plate mesoderm and defect of both hematopoietic and vascular development. Mechanistically, we uncover that Jam3b promotes endothelial specification by regulating npas4l expression through the repression of the Rap1a-Erk signaling cascade. Jam3b subsequently promotes hematopoietic development including HSCs by regulating lrrc15 expression in endothelial precursors through the activation of an integrin-dependent signaling cascade. Our data provide insight into the divergent mechanisms for instructing hematopoietic or vascular fates from mesodermal cells.

developmental biology↗

bioRxiv2019

Translational regulation of protrusion-localized RNAs involves silencing and clustering after transport

Localization of RNAs to various subcellular destinations is a widely used mechanism that regulates a large proportion of transcripts in polarized cells. In many cases, such localized transcripts mediate spatial control of gene expression by being translationally silent while in transit and locally activated at their destination. Here, we investigate the translation of RNAs localized at dynamic cellular protrusions of human and mouse, migrating, mesenchymal cells. In contrast to the model described above, we find that protrusion-localized RNAs are not locally activated solely at protrusions, but can be translated with similar efficiency in both internal and peripheral locations. Interestingly, protrusion-localized RNAs are translated at extending protrusions, they become translationally silenced in retracting protrusions and this silencing is accompanied by coalescence of single RNAs into larger heterogeneous RNA clusters. This work describes a distinct mode of translational regulation of localized RNAs, which we propose is used to regulate protein activities during dynamic cellular responses.

cell biology↗