Biology subjects

Nakazawa, Y.

Publications and source records attributed to Nakazawa, Y..

11 recordsLinked to original sources

bioRxiv2026

PiggyBac transposon and transposase delivered in trans, in cis, and as mRNA for engineering CAR-T cells: a multi-objective optimization

Chimeric antigen receptor (CAR)-T cell therapy has become a revolutionary strategy in cancer immunotherapy. However, conventional manufacturing strategies, which rely on viral vectors to deliver genetic material to host genomes, are hindered by many obstacles that have limited their widespread clinical application. This study aims to optimize the delivery of piggyBac transposon for simple and cost-effective manufacturing of CAR-T cells. We tested three different piggyBac delivery strategies: (i) conventional two-plasmid system (CONV), (ii) helper and donor one-plasmid system (ONE), and (iii) mRNA transposase in combination with a DNA donor plasmid (MRNA). Each method was evaluated for transfection efficiency, cell viability, and transgene copy number. The results demonstrated that, without enrichment, ONE approach generated CAR-T cells with the highest gene delivery efficiency at the cost of lower viability and higher transgene copy number, while transfection using MRNA offered a reduction in transgene copy numbers at the cost of lower efficiency. Interestingly, with enrichment by autologous feeder, the shortcoming in viability was completely overcome while retaining higher efficiency and higher transgene copy number. The result of this study lays the groundwork for a more efficient and safer piggyBac-engineered CAR T cell manufacturing process, and it should facilitate the decision in method selection for further optimization and clinical scale-up.

synthetic biology↗

bioRxiv2026

Historic and contemporary museum specimens implicate Northern Red-backed Vole (Clethrionomys rutilus) as borealpox host as early as 1990s

Borealpox virus (BRPV; formerly Alaskapox) is an orthopoxvirus that has caused seven reported human infections in Alaska since 2015, including a fatal case in 2023. The natural reservoir of BRPV is unknown, although previous investigations have raised the possibility of wild small mammals transmitting the virus to humans, either through direct contact or via domestic cats and dogs. To understand which species may be involved in the maintenance and/or spillover of BRPV in Alaska, we trapped and sampled wild small mammals (including voles, shrews, and squirrels) in 2021 and 2024 near reported human case locations in Fairbanks and the Kenai Peninsula, respectively. We found evidence of previous exposure to orthopoxviruses in five species (including the House Mouse, Mus musculus) and detected BRPV DNA as well as viable virus in Northern Red-backed Voles (Clethrionomys rutilus). Further, screening of tissues from historical museum specimens revealed BRPV DNA in C. rutilus specimens collected in Denali National Park and Preserve in 1998 and 1999, 17 years before the first reported human case of BRPV. Phylogenomic analysis of all human and animal BRPV isolates strongly supports the hypothesis of local human infections through multiple spillover events. These findings suggest C. rutilus as a possible reservoir species for BRPV and indicate that BRPV has been present in Alaskan wild small-mammal populations for at least 25 years. Our study highlights the potential of museum collections to elucidate the temporal, spatial, and host ranges of emerging pathogens. Further museum- and field-based sampling will clarify the true geographic range of BRPV, which is closely related to Old World orthopoxviruses and may be circulating beyond North America.

ecology↗

bioRxiv2026

Oribatid Mites Supply Tetrodotoxin to Poisonous Newts

Tetrodotoxin (TTX) is a potent neurotoxin widely distributed among marine and terrestrial animals, yet how terrestrial vertebrates acquire this toxin has been debated for decades. Here, we identify oribatid mites as the primary dietary sources of TTX for the Japanese fire-bellied newt, Cynops pyrrhogaster. We detect TTX and its analogs in the mites Scheloribates processus and Galumna sp. KM1, which are preferentially consumed by terrestrial newts. In a controlled toxification experiment, juvenile newts accumulated TTX after consuming TTX-bearing mites, directly demonstrating dietary sequestration. Our results demonstrate that the early terrestrial stage is critical for lifelong TTX acquisition in newts. Notably, we also detect pumiliotoxin, a poison-frog alkaloid, in S. processus, suggesting that newts and poison frogs have convergently evolved to exploit toxin-bearing microarthropods for chemical defense. We propose a "terrestrial toxic web" hypothesis in which oribatid mites act as a shared environmental reservoir linking putative microbial toxin production to vertebrate chemical defense, highlighting microarthropods as key mediators in terrestrial toxin flow.

ecology↗

bioRxiv2025

Chlamydomonas γ-tubulin mutations reveal a critical role of γ-TuRC in maintaining the stability of centriolar microtubules

The centriolar triplet microtubule consists of an A-tubule with 13 protofilaments, and B-and C-tubules, each with 10 protofilaments. Although the formation of the triplets has been shown to require {gamma}-tubulin, its specific role in the formation of each tubule remains elusive. We isolated two novel Chlamydomonas reinhardtii mutants, bld13-1 and bld13-2, each expressing {gamma}-tubulin with a single amino-acid substitution (T292I or E89D). Similar to known centriole-deficient mutants, both mutants exhibited defects in ciliary assembly, nuclear number, as well as the number and orientation of cytoplasmic microtubules. Genetic analyses of the mutants, along with the expression of the mutant {gamma}-tubulins in the wild-type cells, suggested that both mutants exert dominant-negative effects over wild-type {gamma}-tubulin. Interestingly, although the centrioles in these mutants retained the typical nine triplet structure, their triplets frequently lacked several protofilaments in specific regions of the A- and C-tubules. The protofilament loss occurs more frequently in the proximal region of the centriole. These structural defects suggest a critical role for {gamma}-tubulin in maintaining the stability of the A- and C-tubules of centriolar triplets. Summary statementNovel Chlamydomonas {gamma}-tubulin mutations cause a partial loss of protofilaments in centriolar microtubules, indicating a critical role of {gamma}-tubulin in structural stabilization of triplet microtubules.

cell biology↗

bioRxiv2024

Enhanced anti-tumor effects through continuous administration of engineered CAR-macrophages derived from pluripotent stem cell-derived myeloid celllines.

Even after chimeric antigen receptor (CAR)-based immunotherapy has dramatically changed therapeutic approaches for malignancies, balancing therapeutic efficacy with labor and financial cost remains a major problem for immunotherapy. Current study developed a cost-effective and enhanced approach to chimeric antigen receptor (CAR)-macrophage therapy for cancer and demonstrated its therapeutic effects by repeated administration of anti-HER2 CAR macrophages generated from human pluripotent stem cell (PSC)-derived immortalized myeloid cell lines (ML). These ML-derived CAR macrophages (CAR-ML-MPs) exhibit potent antigen-specific killing activity against HER2-expressing tumor cells by phagocytosis in vitro and effectively inhibit tumor progression in vivo, which is enhanced by repeated administration. CAR-ML-MPs provide a promising off-the-shelf cellular resource for tumor adoptive cell immunotherapy, solving the cost and time problems associated with conventional CAR-based immunotherapy.

bioengineering↗

bioRxiv2024

Clearance of DNA damage-arrested RNAPII is selectively impaired in Cockayne syndrome cells

Arrest of elongating RNA polymerase II (RNAPII) at DNA lesions initiates transcription-coupled repair (TCR), involving the concerted action of specific TCR factors, followed by downstream nucleotide excision repair steps. Remarkedly, only congenital defects in the CSA or CSB genes cause the neurodegenerative disorder Cockayne syndrome, which is not observed with other TCR genes, despite their equal importance in TCR. An explanation for this discrepancy has been lacking. In this study, we developed an assay to track the fate of elongating RNAPII at sites of UV-induced DNA lesions. Employing this method on an isogenic collection of TCR knockout cells reveals a selective RNAPII clearance defect in cells defective in CSA or CSB, in contrast to knockouts of other TCR genes. Our findings provide evidence that a deficiency in RNAPII processing and prolonged transcription arrests in response to DNA damage, rather than compromised DNA repair, may underlie the Cockayne syndrome-like neurodegenerative phenotype.

cell biology↗

bioRxiv2024

A beta-Galactosidase acting on unique galactosides: the structure and function of a beta-1,2-galactosidase from Bacteroides xylanisolvens, an intestinal bacterium

Galactosides are major carbohydrates that are found in plant cell walls and various prebiotic oligosaccharides. Studying the detailed biochemical functions of {beta}-galactosidases in degrading these carbohydrates is important. In particular, identifying {beta}-galactosidases with new substrate specificities could help in the production of potentially beneficial oligosaccharides. In this study, we identified a {beta}-galactosidase with novel substrate specificity from Bacteroides xylanisolvens, an intestinal bacterium. The enzyme did not show hydrolytic activity toward natural {beta}-galactosides during the first screening. However, when -D-galactosyl fluoride (-GalF) as a donor substrate and galactose or D-fucose as an acceptor substrate were incubated with a nucleophile mutant, reaction products were detected. The galactobiose produced from the -GalF and galactose was identified as {beta}-1,2-galactobiose using NMR. Kinetic analysis revealed that this enzyme effectively hydrolyzed {beta}-1,2-galactobiose and {beta}-1,2-galactotriose. In the complex structure with methyl {beta}-galactopyranose as a ligand, the ligand is only located at subsite +1. The 2-hydroxy group and the anomeric methyl group of methyl {beta}-galactopyranose faces in the direction of subsite -1 and the solvent, respectively. This observation is consistent with the substrate specificity of the enzyme regarding linkage position and chain length. Overall, we concluded that the enzyme is a {beta}-galactosidase acting on {beta}-1,2-galactooligosaccharides. SynopsisThe structural and functional analysis of {beta}-galactosidase from an intestinal bacterium led to the discovery of a new {beta}-galactosidase hydrolyzing unique {beta}-1,2-galactooligosaccharides.

biochemistry↗

bioRxiv2021

Cluster Analysis of SARS-CoV-2 Gene using Deep Learning Autoencoder: Gene Profiling for Mutations and Transitions

We report on a method for analyzing the variant of coronavirus genes using autoencoder. Since coronaviruses have mutated rapidly and generated a large number of genotypes, an appropriate method for understanding the entire population is required. The method using autoencoder meets this requirement and is suitable for understanding how and when the variants emarge and disappear. For the over 30,000 SARS-CoV-2 ORF1ab gene sequences sampled globally from December 2019 to February 2021, we were able to represent a summary of their characteristics in a 3D plot and show the expansion, decline, and transformation of the virus types over time and by region. Based on ORF1ab genes, the SARS-CoV-2 viruses were classified into five major types (A, B, C, D, and E in the order of appearance): the virus type that originated in China at the end of 2019 (type A) practically disappeared in June 2020; two virus types (types B and C) have emerged in the United States and Europe since February 2020, and type B has become a global phenomenon. Type C is only prevalent in the U.S. and is suspected to be associated with high mortality, but this type also disappeared at the end of June. Type D is only found in Australia. Currently, the epidemic is dominated by types B and E.

microbiology↗

bioRxiv2021

ELOF1 is a transcription-coupled DNA repair factor that directs RNA polymerase II ubiquitylation

Cells employ transcription-coupled repair (TCR) to eliminate transcription-blocking DNA lesions. The binding of the TCR-specific repair factor CSB triggers DNA damage-induced ubiquitylation of RNA polymerase II (RNAPII) at a single lysine (K1268) by the CRL4CSA ubiquitin ligase. However, how the CRL4CSA ligase is specifically directed toward the K1268 site is unknown. Here, we identify ELOF1 as the missing link that facilitates RNAPII ubiquitylation, a key signal for the assembly of downstream repair factors. This function requires its constitutive interaction with RNAPII close to the K1268 site, revealing ELOF1 as a specificity factor that positions CRL4CSA for optimal RNAPII ubiquitylation. Furthermore, drug-genetic interaction screening reveals an unanticipated compensatory TCR pathway in which ELOF1 together with known factors DOT1L and HIRA protect CSB-deficient cells from collisions between transcription and replication machineries. Our study provides a genetic framework of the transcription stress response and reveals key insights into the molecular mechanism of TCR.

molecular biology↗

bioRxiv2020

Tumor-derived extracellular vesicles regulate tumor-infiltrating regulatory T cells via the immunoreceptor CD300a

Although tumor-infiltrating regulatory T (Treg) cells play a pivotal role in tumor immunity, how Treg cell activation are regulated in tumor microenvironments remains unclear. Here, we found that mice deficient in the inhibitory immunoreceptor CD300a on their dendritic cells (DCs) have increased numbers of Treg cells in tumors and greater tumor growth compared with wild-type mice after transplantation of B16 melanoma. Pharmacological impairment of extracellular vesicle (EV) release decreased Treg cell numbers in CD300a-deficient mice. Coculture of DCs with tumor-derived EV (TEV) induced the internalization of CD300a and the incorporation of EVs into endosomes, in which CD300a inhibited TEV-mediated TLR3-TRIF signaling for activation of the IFN-{beta}-Treg cells axis. We also show that higher expression of CD300A was associated with decreased tumor-infiltrating Treg cells and longer survival time in patients with melanoma. Our findings reveal the role of TEV and CD300a on DCs in Treg cell activation in the tumor microenvironment.

cancer biology↗

bioRxiv2020

Genome sequence of Hydrangea macrophylla and its application in analysis of the double flower phenotype

Owing to its high ornamental value, the double flower phenotype of hydrangea (Hydrangea macrophylla) is one of its most important traits. In this study, genome sequence information was obtained to explore effective DNA markers and the causative genes for double flower production in hydrangea. Single molecule real-time sequencing data followed by a HiC analysis was employed. The resultant haplotype-phased sequences consisted of 3,779 sequences (2.256 Gb in length and N50 of 1.5 Mb), and 18 pseudomolecules comprising 1.08 Gb scaffold sequences along with a high-density SNP genetic linkage map. Using the genome sequence data obtained from two breeding populations, the SNPs linked to double flower loci (Djo and Dsu), were discovered for each breeding population. DNA markers J01 linked to Djo and S01 linked to Dsu were developed, and these could be used successfully to distinguish the recessive double flower allele for each locus respectively. The LEAFY gene was suggested as the causative gene for Dsu, since frameshift was specifically observed in double flower accession with dsu. The genome information obtained in this study will facilitate a wide range of genomic studies on hydrangea in the future.

genomics↗