Development of basic technology for spatial genomics of in three-dimensional tissues

• Project/Area Number: 18K19419
• Research Category: Grant-in-Aid for Challenging Research (Exploratory)
• Allocation Type: Multi-year Fund
• Review Section: Medium-sized Section 48:Biomedical structure and function and related fields
• Research Institution: The University of Tokyo
• Principal Investigator: Susaki Etsuo 東京大学, 大学院医学系研究科(医学部), 准教授 (10444803)
• Project Period (FY): 2018-06-29 – 2020-03-31
• Project Status: Completed (Fiscal Year 2019)
• Budget Amount: ¥6,370,000 (Direct Cost: ¥4,900,000、Indirect Cost: ¥1,470,000); Fiscal Year 2019: ¥5,070,000 (Direct Cost: ¥3,900,000、Indirect Cost: ¥1,170,000); Fiscal Year 2018: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
• Keywords: 多階層オミクス / 組織透明化 / 3次元イメージング / 核酸解析

Outline of Final Research Achievements

We tried to develop a technology for spatial genomics to obtain the genome profile of each cell after recording all nuclear positions in the three-dimensional tissue. We have successfully developed an advanced tissue clearing method that covers the whole organ. (Cell Rep 2018). In addition, we elucidated the principle of nuclear stain penetration based on the tissue's physicochemical properties. We finally constructed a uniform nuclear staining protocol for large organ samples. Using a developed gel embedding method of cleared samples, we also successfully imaged the whole organ and acquired the cell nucleus voxel's position using light-sheet microscopes. We summarized these results and submitted them in a paper (Nat Commun, submitted; published after the close of the project).

Academic Significance and Societal Importance of the Research Achievements

本研究成果ではこれまで実証例のない空間的ゲノミクス実現に向けた重要な技術課題を克服し、がん、老化、発生等におけるゲノム情報と空間位置情報との関連を紐付けながら組織・臓器の構築や極めて少数の細胞種・細胞状態を同定できる新しい研究スキームの提示が期待できる。また、本研究成果で得られた新しい核染色プロトコルは、これまで解決されていなかった染色剤の浸透原理を解明し、ボトムアップなデザインを実現した。このように組織の物理化学的性質に基づいたプロトコルデザインは、今後の組織学的手法の構築に重要な方向性を示すものになるとともに、3次元病理学の実現による診断確度や客観性向上に大きく貢献するものと期待される。

Research Products

• [Journal Article] Visualization and molecular characterization of whole-brain vascular networks with capillary resolution. (2020)
  • Author(s): Takeyuki Miyawaki,Shota Morikawa,Etsuo A Susaki,Ai Nakashima,Haruki Takeuchi,Shun Yamaguchi,Hiroki R Ueda,Yuji Ikegaya
  • Journal Title: Nature communications Volume: 11 Issue: 1 Pages: 1104-1104
  • DOI: 10.1038/s41467-020-14786-z
  • Peer Reviewed / Open Access
• [Journal Article] Novel 3D analysis using optical tissue clearing documents the evolution of murine rapidly progressive glomerulonephritis (2019)
  • Author(s): Puelles VG, Fleck D, Ortz L, Papadouri S, Thiago T, Boehner A, van der Wolde JW, Vogt M, Saritas T, Kuppe C, Fuss A, Menzel S, Klinkhammer BM, Mller-Newen G, Heymann F, Decker L, Braun F, Kretz O, Huber TB, Susaki EA, Ueda HR, et al.
  • Journal Title: Kidney international Volume: AOP Issue: 2 Pages: 505-516
  • DOI: 10.1016/j.kint.2019.02.034
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Comprehensive three-dimensional analysis (CUBIC-kidney) visualizes abnormal renal sympathetic nerves after ischemia/reperfusion injury. (2019)
  • Author(s): Hasegawa S, Susaki EA, Tanaka T, Komaba H, Wada T, Fukagawa M, Ueda HR, Nangaku M
  • Journal Title: Kidney international Volume: AOP Issue: 1 Pages: 129-138
  • DOI: 10.1016/j.kint.2019.02.011
  • Peer Reviewed
• [Journal Article] 【バイオマテリアル研究に役立つ分析技術・評価法】生体組織の透明化とイメージング技術 (2019)
  • Author(s): 吉田 将太,松本 桂彦,洲崎 悦生,上田 泰己
  • Journal Title: バイオマテリアル-生体材料- Volume: 37 Pages: 264-269
• [Journal Article] CUBICを用いた組織透明化と3次元観察 (2019)
  • Author(s): 洲崎悦生
  • Journal Title: 和光純薬時報 Volume: 87 Pages: 16-19
• [Journal Article] 人工知能と神経科学 病理画像の自動診断技術と3次元病理学の発展 (2019)
  • Author(s): 洲崎悦生
  • Journal Title: Brain and Nerve Volume: 71
• [Journal Article] 透明イメージングの臨床応用 組織透明化技術と細胞ラベリング技術 (2019)
  • Author(s): 洲崎悦生
  • Journal Title: 月刊メディカル・サイエンス・ダイジェスト Volume: 45
• [Journal Article] Chemical Landscape for Tissue Clearing Based on Hydrophilic Reagents. (2018)
  • Author(s): Tainaka K, Murakami TC, Susaki EA, Shimizu C, Saito R, Takahashi K, Hayashi-Takagi A, Sekiya H, Arima Y, Nojima S, Ikemura M, Ushiku T, Shimizu Y, Murakami M, Tanaka KF, Iino M, Kasai H, Sasaoka T, Kobayashi K, Miyazono K, Morii E, Isa T, Fukayama M, Kakita A, Ueda HR.
  • Journal Title: Cell Rep. Volume: 24 Issue: 8 Pages: 2196-2210
  • DOI: 10.1016/j.celrep.2018.07.056
  • NAID: 120006542018
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Comparison of the 3-D patterns of the parasympathetic nervous system in the lung at late developmental stages between mouse and chicken (2018)
  • Author(s): Watanabe Tadayoshi、Nakamura Ryo、Takase Yuta、Susaki Etsuo A.、Ueda Hiroki R.、Tadokoro Ryosuke、Takahashi Yoshiko
  • Journal Title: Developmental Biology Volume: 444 Pages: S325-S336
  • DOI: 10.1016/j.ydbio.2018.05.014
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] 見る脂質のページ〈透明化による全細胞解析〉ヒト組織透明化 ~ヒト病理組織を中心に~ (2018)
  • Author(s): 野島聡、森井英一、洲崎悦生、上田泰己
  • Journal Title: Lipid Volume: 29 Pages: 340-345
• [Journal Article] 快人快説 最先端の研究テクノロジー紹介?臓器の透明化技術とその臨床応用 (2018)
  • Author(s): 野島聡、洲崎悦生、森井英一、上田泰己
  • Journal Title: LiSA Volume: 25 Pages: 789-797
• [Journal Article] 見る脂質のページ〈脂質代謝異常〉脱脂による高度な全脳透明化と三次元イメージング (2018)
  • Author(s): 洲崎悦生
  • Journal Title: Lipid Volume: 29 Pages: 128-134
• [Presentation] セルオミクスによる多細胞システム解明へのアプローチ (2019)
  • Author(s): 洲崎悦生
  • Organizer: 岡山大学次世代研究拠点シンポジウム2020「口腔器官の再構築から器官の発生・再生の統一原理の解明」
  • Invited
• [Presentation] A versatile three-dimensional whole-organ/body staining and imaging with single-cell resolution based on electrolyte-gel properties of biological tissue (2019)
  • Author(s): 洲崎悦生
  • Organizer: The Light Sheet Microscopy Conference 2019
  • Int'l Joint Research
• [Presentation] A versatile protocol for three-dimensional whole-organ/body staining and imaging with single-cell resolution based on electrolyte-gel properties of biological tissue. (2019)
  • Author(s): Susaki EA et al.
  • Organizer: Society for Neuroscience 2019
  • Int'l Joint Research
• [Presentation] 組織透明化技術の開発と医学生物学応用（モーニングレクチャー） (2019)
  • Author(s): 洲崎悦生
  • Organizer: 第78回日本癌学会学術総会
  • Invited
• [Presentation] 全臓器・全身スケールの多階層空間オミクス実現に向けたアプローチ (2019)
  • Author(s): 洲崎悦生
  • Organizer: シングルセルゲノミクス研究会2019
  • Invited
• [Presentation] 全臓器・全身の細胞ダイバーシティー解明を目指す臓器スケール3次元組織学への挑戦 (2019)
  • Author(s): 洲崎悦生
  • Organizer: 第19回日本蛋白質科学会年会・第71回日本細胞生物学会大会 合同年次大会 共催シンポジウム「総力戦でのぞむ細胞社会ダイバーシティー解明への挑戦」（兼オーガナイザー）
• [Presentation] CUBIC-HistoVIsion: A pipeline for three-dimensional whole-organ staining and imaging with single-cell resolution based on chemical properties of tissue (2019)
  • Author(s): 洲崎悦生
  • Organizer: RIKEN BDR seminar at Kobe (host: Dr. Kazunari Miyamichi)
• [Presentation] 組織3D染色による細胞の網羅的解析技術の開発 (2019)
  • Author(s): 洲崎悦生
  • Organizer: JSTさきがけ・統合1細胞領域 第4回成果報告会（日本化学会第99回春季年会2019 コラボレイション企画）
• [Presentation] CUBIC-HistoVIsion: a pipeline for three-dimensional whole-organ/body staining and imaging with single-cell resolution based on chemical properties of tissue gel (2019)
  • Author(s): 洲崎悦生
  • Organizer: Visiting seminar at Oxford University, UK (host: Host: Dr Ana Domingos)
  • Int'l Joint Research
• [Presentation] CUBIC-HistoVIsion: a pipeline for three-dimensional whole-organ/body staining and imaging with single-cell resolution based on chemical properties of tissue gel (2019)
  • Author(s): 洲崎悦生
  • Organizer: Visiting seminar at Science for Life Laboratory (KTH), Sweden (host: Prof. Hans Blom)
  • Int'l Joint Research
• [Presentation] Whole-organ/body analysis of multicellular systems by CUBIC platform (2019)
  • Author(s): 洲崎悦生
  • Organizer: Single cell biology meets diagnostics: 12th International workshop on approaches to single cell analysis, Uppsala University, Sweden
  • Int'l Joint Research / Invited
• [Presentation] CUBIC-HistoVIsion: a pipeline for three-dimensional whole-organ/body staining and imaging with single-cell resolution based on chemical properties of tissue gel (2019)
  • Author(s): 洲崎悦生
  • Organizer: Bioscience seminar (visiting seminar), Uppsala University, Sweden (Host: Prof. Ola S?derberg)
  • Int'l Joint Research
• [Presentation] 細胞ネットワークの網羅的解析～個体をシステムとして理解するアイデアと方法 (2018)
  • Author(s): 洲崎悦生
  • Organizer: 順天堂大学医学部「医学研究入門II」講義
• [Presentation] 多細胞システムの状態定義・分離を目指す技術開発 (2018)
  • Author(s): 洲崎悦生
  • Organizer: 第41回日本分子生物学会年会
• [Presentation] CUBIC-HistoVIsion: a pipeline for three-dimentional whole-brain/organ staining and imaging with single-cell resolution (2018)
  • Author(s): 洲崎悦生
  • Organizer: ECRO 2018
  • Int'l Joint Research / Invited
• [Presentation] 多細胞システムの理解に向けた要素技術開発と展望 (2018)
  • Author(s): 洲崎悦生
  • Organizer: 第58回 生命科学夏の学校
  • Invited
• [Presentation] 網羅的細胞観察・解析技術による、多細胞システム解明への挑戦 (2018)
  • Author(s): 洲崎悦生
  • Organizer: 第５回包括的緩和医療科学学術研究会/第６回Tokyo疼痛緩和次世代研究会 合同研究会
  • Invited
• [Presentation] Tissue clearing and 3D imaging: basics and applications (2018)
  • Author(s): 洲崎悦生
  • Organizer: EMBO practical course on light sheet microscopy
  • Int'l Joint Research / Invited
• [Presentation] CUBIC-HistoVIsion: a pipeline for 3D whole-organ/body staining and imaging with single-cell resolution based on chemical properties of tissue gel (2018)
  • Author(s): 洲崎悦生
  • Organizer: SBIC seminar, A*STAR, Singapore
  • Int'l Joint Research / Invited
• [Presentation] 個体レベルのシステム生物学実現を目指す技術開発 (2018)
  • Author(s): 洲崎悦生
  • Organizer: 第91回日本内分泌学会学術総会 中堅・若手の会YEC企画2「生体リズム研究の新展開」
  • Invited
• [Book] バイオイノベーションに向けて～バイオテクノロジーの新技術からの新しい視点～ 監修： 植田充美 (2019)
  • Author(s): 洲崎悦生 他（分担執筆）
  • Total Pages: 258
  • Publisher: (株)シーエムシー出版
  • ISBN: 9784781314112
• [Book] 定量生物学-生命現象を定量的に理解するために 小林徹也／編 (2018)
  • Author(s): 洲崎悦生 他（分担執筆）
  • Total Pages: 290
  • Publisher: 化学同人
  • ISBN: 9784759817300
• [Remarks] 臓器透明化（CUBIC）を用いて腎臓全体の交感神経系の3次元構造を可視化し、その機能障害を解析
  • URL: http://www.h.u-tokyo.ac.jp/press/press_archives/20190409.html
• [Remarks] 水溶性化合物による組織透明化の化学 －包括的ケミカルプロファイリングに基づく化学的原理の体系化－
  • URL: http://www.riken.jp/pr/press/2018/20180822_1/