Chemical Landscape for Tissue Clearing Based on Hydrophilic Reagents

Kazuki Tainaka; Tatsuya C Murakami; Etsuo A Susaki; Chika Shimizu; Rie Saito; Kei Takahashi; Akiko Hayashi-Takagi; Hiroshi Sekiya; Yasunobu Arima; Satoshi Nojima; Masako Ikemura; Tetsuo Ushiku; Yoshihiro Shimizu; Masaaki Murakami; Kenji F Tanaka; Masamitsu Iino; Haruo Kasai; Toshikuni Sasaoka; Kazuto Kobayashi; Kohei Miyazono; Eiichi Morii; Tadashi Isa; Masashi Fukayama; Akiyoshi Kakita; Hiroki R Ueda

doi:10.1016/j.celrep.2018.07.056

Chemical Landscape for Tissue Clearing Based on Hydrophilic Reagents

Cell Rep. 2018 Aug 21;24(8):2196-2210.e9. doi: 10.1016/j.celrep.2018.07.056.

Authors

Kazuki Tainaka¹, Tatsuya C Murakami², Etsuo A Susaki³, Chika Shimizu⁴, Rie Saito⁵, Kei Takahashi⁶, Akiko Hayashi-Takagi⁷, Hiroshi Sekiya⁸, Yasunobu Arima⁹, Satoshi Nojima¹⁰, Masako Ikemura¹¹, Tetsuo Ushiku¹¹, Yoshihiro Shimizu¹², Masaaki Murakami⁹, Kenji F Tanaka¹³, Masamitsu Iino¹⁴, Haruo Kasai¹⁵, Toshikuni Sasaoka¹⁶, Kazuto Kobayashi¹⁷, Kohei Miyazono⁶, Eiichi Morii¹⁰, Tadashi Isa¹⁸, Masashi Fukayama¹¹, Akiyoshi Kakita⁵, Hiroki R Ueda¹⁹

Affiliations

¹ Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka 565-5241, Japan; Department of System Pathology for Neurological Disorders, Brain Research Institute, Niigata University, 1-757 Asahimachidori, Chuo-ku, Niigata 951-8585, Japan.
² Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
³ Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka 565-5241, Japan; PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
⁴ Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka 565-5241, Japan.
⁵ Department of Pathology, Brain Research Institute, Niigata University, 1-757 Asahimachidori, Chuo-ku, Niigata 951-8585, Japan.
⁶ Department of Molecular Pathology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
⁷ PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan; Laboratory of Medical Neuroscience, Institute for Molecular and Cellular Regulation, Gunma University, 3-39-15 Showacho, Maebashi, Gunma 371-8512, Japan.
⁸ Department of Pharmacology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
⁹ Division of Psychoimmunology, Institute of Genetic Medicine, Graduate School of Medicine, Hokkaido University, Kita-15, Nishi-7, Kita-ku, Sapporo, Hokkaido 060-0815, Japan.
¹⁰ Department of Pathology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
¹¹ Department of Pathology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
¹² Laboratory for Cell-Free Protein Synthesis, RIKEN Center for Biosystems Dynamics Research, 6-2-3, Furuedai, Suita, Osaka 565-0874, Japan.
¹³ Department of Neuropsychiatry, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan.
¹⁴ Department of Pharmacology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Division of Cellular and Molecular Pharmacology, Nihon University School of Medicine, 30-1 Oyaguchikami-cho, Itabashi-ku, Tokyo 173-8610, Japan.
¹⁵ Laboratory of Structural Physiology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; International Research Center for Neurointelligence (WPI-IRCN), UTIAS, The University of Tokyo, Tokyo, Japan.
¹⁶ Department of Comparative and Experimental Medicine, Brain Research Institute, Niigata University, 1-757 Asahimachidori, Chuo-ku, Niigata 951-8585, Japan.
¹⁷ Department of Molecular Genetics, Institute of Biomedical Sciences, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, Fukushima 960-1295, Japan.
¹⁸ Department of Neuroscience, Graduate School of Medicine and Faculty of Medicine, Kyoto University, Yoshida-konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.
¹⁹ Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka 565-5241, Japan; International Research Center for Neurointelligence (WPI-IRCN), UTIAS, The University of Tokyo, Tokyo, Japan. Electronic address: uedah-tky@umin.ac.jp.

PMID: 30134179
DOI: 10.1016/j.celrep.2018.07.056

Abstract

We describe a strategy for developing hydrophilic chemical cocktails for tissue delipidation, decoloring, refractive index (RI) matching, and decalcification, based on comprehensive chemical profiling. More than 1,600 chemicals were screened by a high-throughput evaluation system for each chemical process. The chemical profiling revealed important chemical factors: salt-free amine with high octanol/water partition-coefficient (logP) for delipidation, N-alkylimidazole for decoloring, aromatic amide for RI matching, and protonation of phosphate ion for decalcification. The strategic integration of optimal chemical cocktails provided a series of CUBIC (clear, unobstructed brain/body imaging cocktails and computational analysis) protocols, which efficiently clear mouse organs, mouse body including bone, and even large primate and human tissues. The updated CUBIC protocols are scalable and reproducible, and they enable three-dimensional imaging of the mammalian body and large primate and human tissues. This strategy represents a future paradigm for the rational design of hydrophilic clearing cocktails that can be used for large tissues.

Keywords: chemistry in tissue clearing; comprehensive chemical profiling; high-throughput chemical screening; hydrophilic reagents; three-dimensional imaging; virtual multiplex imaging.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Humans
Hydrophobic and Hydrophilic Interactions
Indicators and Reagents / chemistry*

Substances

Indicators and Reagents