Biology subjects

Tsuboi, A.

Publications and source records attributed to Tsuboi, A..

3 recordsLinked to original sources

bioRxiv2023

Spatio-temporal remodeling of extracellular matrix orients epithelial sheet folding

Biological systems are inherently noisy; however, they produce highly stereotyped tissue morphology. Drosophila pupal wings show a highly stereotypic folding through uniform expansion and subsequent buckling of wing epithelium within a surrounding cuticle sac. The folding pattern produced by buckling is generally stochastic; it is thus unclear how buckling leads to stereotypic tissue folding of the wings. We found that the extracellular matrix (ECM) protein, Dumpy, guides the position and direction of buckling-induced folds. Dumpy anchors the wing epithelium to the overlying cuticle at specific tissue positions. Tissue-wide alterations of Dumpy deposition and degradation yielded different buckling patterns. In summary, we propose that spatio-temporal ECM remodeling shapes stereotyped tissue folding through dynamic interactions between the epithelium and its external structures. One-Sentence SummaryRemodeling of extracellular matrix protein, Dumpy, guides epithelial tissue folding during Drosophila wing development.

developmental biology↗

bioRxiv2021

T cell-intrinsic vitamin A metabolism and its signaling are targets for memory T cell-based cancer immunotherapy

Memory T cells play an essential role in infectious and tumor immunity. Vitamin A metabolites such as retinoic acid are immune modulators, but the role of vitamin A metabolism in memory T- cell differentiation is unclear. In this study, we identified retinol dehydrogenase 10 (Rdh10), which metabolizes vitamin A to retinal (RAL), as a key molecule for regulating T cell differentiation. T cell-specific Rdh10 deficiency enhanced memory T-cell formation through blocking RAL production in infection model. Epigenetic profiling revealed that retinoic acid receptor (RAR) signaling activated by vitamin A metabolites induced comprehensive epigenetic repression of memory T cell-associated genes, including TCF7, thereby promoting effector T-cell differentiation. Importantly, memory T cells generated by Rdh10 deficiency and blocking RAR signaling elicited potent anti-tumor responses in adoptive T-cell transfer setting. Thus, T cell differentiation is regulated by vitamin A metabolism and its signaling, which should be novel targets for memory T cell-based cancer immunotherapy.

immunology↗

bioRxiv2017

Mapping-based all-RNA-information sequencing analysis (ARIseq) pipeline simultaneously revealed taxonomic composition, gene expression, and their correlation in an acidic stream ecosystem

We developed a new pipeline for simultaneous analyses of both rRNA profile as a taxonomic marker and mRNA profile as a functional marker, to understand microbial ecosystems in natural environments. Our pipeline, named All-RNA-Information sequencing (ARIseq), comprises a high-throughput sequencing of reverse transcribed total RNA and several widely used computational tools, and generates quantitatively reliable information on both community structures and gene expression patterns, which were verified by quantitative PCR analyses in this study. Particularly, correlation network analysis in the pipeline can reveal microbial taxa and expressed genes that share patterns of dynamics among different time and/or geographical points. The pipeline is primarily mapping-based, using a public database for small subunit rRNA genes and obtained contigs as the reference database for protein-coding genes. We applied this pipeline to biofilm samples, as examples, collected from an acidic spring water stream in the Chyatsubomi-goke Park in Gunma prefecture, Japan. Our analyses revealed the predominance of iron and sulfur-oxidizing bacteria and Pinnularia diatoms, and also indicated that the distributions of the iron-sulfur-oxidizing bacterial consortium and the Pinnularia diatoms largely overlapped but showed distinct patterns. In addition, our analyses showed that the iron-oxidizing bacterial genus Acidithiobacillus and co-occurring Acidiphilium shared similar distribution pattern whereas another iron-oxidizing genus Leptospirillum exhibited a distinct pattern. Our pipeline enables researchers to more easily capture the outline of microbial ecosystems based on the taxonomic composition, protein-coding gene expression, and their correlations.

microbiology↗