Whole-brain spatial transcriptional analysis at cellular resolution

IF 44.7 1区综合性期刊 Q1 MULTIDISCIPLINARY SCIENCES

Science Pub Date : 2024-11-21 DOI:10.1126/science.adn9947

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}

引用次数: 0

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.

查看原文本刊更多论文

细胞分辨率的全脑空间转录分析

RNA 分析的最新进展加深了我们对生物组织细胞状态的了解。然而，在将 RNA 表达数据与各器官的空间背景相结合方面仍存在很大差距，这主要是由于在完整组织体积内检测 RNA 所面临的挑战。在这里，我们开发了特里斯缓冲液介导的原位杂交链反应信号在清除器官中的保留（TRISCO），这是一种有效的组织清除方法，设计用于全脑空间三维（3D）RNA成像。TRISCO 解决了几个关键问题，包括保持 RNA 的完整性、实现均匀的 RNA 标记和提高组织透明度。我们使用各种细胞身份标记、非编码和活性依赖性 RNA 测试了 TRISCO 在不同大小和物种的器官中的应用。TRISCO 因此成为单细胞、全脑三维成像的强大工具，可对整个大脑进行全面的转录空间分析。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

Science 综合性期刊-综合性期刊

CiteScore

61.10

自引率

0.90%

发文量

审稿时长

2.1 months

期刊介绍： Science is a leading outlet for scientific news, commentary, and cutting-edge research. Through its print and online incarnations, Science reaches an estimated worldwide readership of more than one million. Science’s authorship is global too, and its articles consistently rank among the world's most cited research. Science serves as a forum for discussion of important issues related to the advancement of science by publishing material on which a consensus has been reached as well as including the presentation of minority or conflicting points of view. Accordingly, all articles published in Science—including editorials, news and comment, and book reviews—are signed and reflect the individual views of the authors and not official points of view adopted by AAAS or the institutions with which the authors are affiliated. Science seeks to publish those papers that are most influential in their fields or across fields and that will significantly advance scientific understanding. Selected papers should present novel and broadly important data, syntheses, or concepts. They should merit recognition by the wider scientific community and general public provided by publication in Science, beyond that provided by specialty journals. Science welcomes submissions from all fields of science and from any source. The editors are committed to the prompt evaluation and publication of submitted papers while upholding high standards that support reproducibility of published research. Science is published weekly; selected papers are published online ahead of print.