Shigeaki Kanatani, Judith C. Kreutzmann, Yue Li, Zoe West, Lea Lydolph Larsen, Danai Vougesi Nikou, Ilse Eidhof, Abigail Walton, Songbai Zhang, Leslie Rubio Rodríguez-Kirby, Jacob Lercke Skytte, Casper Gravesen Salinas, Kimiharu Takamatsu, Xiaofei Li, Daisuke H. Tanaka, Dagmara Kaczynska, Keishiro Fukumoto, Razieh Karamzadeh, Yujiao Xiang, Naofumi Uesaka, Tsutomu Tanabe, Mikael Adner, Johan Hartman, Ayako Miyakawa, Erik Sundström, Gonçalo Castelo-Branco, Urmas Roostalu, Jacob Hecksher-Sørensen, Per Uhlén
{"title":"Whole-brain spatial transcriptional analysis at cellular resolution","authors":"Shigeaki Kanatani, Judith C. Kreutzmann, Yue Li, Zoe West, Lea Lydolph Larsen, Danai Vougesi Nikou, Ilse Eidhof, Abigail Walton, Songbai Zhang, Leslie Rubio Rodríguez-Kirby, Jacob Lercke Skytte, Casper Gravesen Salinas, Kimiharu Takamatsu, Xiaofei Li, Daisuke H. Tanaka, Dagmara Kaczynska, Keishiro Fukumoto, Razieh Karamzadeh, Yujiao Xiang, Naofumi Uesaka, Tsutomu Tanabe, Mikael Adner, Johan Hartman, Ayako Miyakawa, Erik Sundström, Gonçalo Castelo-Branco, Urmas Roostalu, Jacob Hecksher-Sørensen, Per Uhlén","doi":"10.1126/science.adn9947","DOIUrl":null,"url":null,"abstract":"<div >Recent advances in RNA analysis have deepened our understanding of cellular states in biological tissues. However, a substantial gap remains in integrating RNA expression data with spatial context across organs, primarily owing to the challenges associated with RNA detection within intact tissue volumes. Here, we developed Tris buffer–mediated retention of in situ hybridization chain reaction signal in cleared organs (TRISCO), an effective tissue-clearing method designed for whole-brain spatial three-dimensional (3D) RNA imaging. TRISCO resolved several crucial issues, including the preservation of RNA integrity, achieving uniform RNA labeling, and enhancing tissue transparency. We tested TRISCO using a broad range of cell-identity markers, noncoding and activity-dependent RNAs, within diverse organs of varying sizes and species. TRISCO thus emerges as a powerful tool for single-cell, whole-brain, 3D imaging that enables comprehensive transcriptional spatial analysis across the entire brain.</div>","PeriodicalId":21678,"journal":{"name":"Science","volume":"386 6724","pages":""},"PeriodicalIF":44.7000,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.science.org/doi/reader/10.1126/science.adn9947","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Science","FirstCategoryId":"103","ListUrlMain":"https://www.science.org/doi/10.1126/science.adn9947","RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"MULTIDISCIPLINARY SCIENCES","Score":null,"Total":0}
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Abstract
Recent advances in RNA analysis have deepened our understanding of cellular states in biological tissues. However, a substantial gap remains in integrating RNA expression data with spatial context across organs, primarily owing to the challenges associated with RNA detection within intact tissue volumes. Here, we developed Tris buffer–mediated retention of in situ hybridization chain reaction signal in cleared organs (TRISCO), an effective tissue-clearing method designed for whole-brain spatial three-dimensional (3D) RNA imaging. TRISCO resolved several crucial issues, including the preservation of RNA integrity, achieving uniform RNA labeling, and enhancing tissue transparency. We tested TRISCO using a broad range of cell-identity markers, noncoding and activity-dependent RNAs, within diverse organs of varying sizes and species. TRISCO thus emerges as a powerful tool for single-cell, whole-brain, 3D imaging that enables comprehensive transcriptional spatial analysis across the entire brain.
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