TY - JOUR
T1 - Chemical Landscape for Tissue Clearing Based on Hydrophilic Reagents
AU - Tainaka, Kazuki
AU - Murakami, Tatsuya C.
AU - Susaki, Etsuo A.
AU - Shimizu, Chika
AU - Saito, Rie
AU - Takahashi, Kei
AU - Hayashi-Takagi, Akiko
AU - Sekiya, Hiroshi
AU - Arima, Yasunobu
AU - Nojima, Satoshi
AU - Ikemura, Masako
AU - Ushiku, Tetsuo
AU - Shimizu, Yoshihiro
AU - Murakami, Masaaki
AU - Tanaka, Kenji F.
AU - Iino, Masamitsu
AU - Kasai, Haruo
AU - Sasaoka, Toshikuni
AU - Kobayashi, Kazuto
AU - Miyazono, Kohei
AU - Morii, Eiichi
AU - Isa, Tadashi
AU - Fukayama, Masashi
AU - Kakita, Akiyoshi
AU - Ueda, Hiroki R.
N1 - Funding Information:
We thank all of the laboratory members at The University of Tokyo and RIKEN Quantitative Biology Center (QBiC), in particular, K. Yoshida for help with the polynomial regression; S. Shi, G.A. Sunagawa, and R.G. Yamada for statistical analysis; and R. Ohno for housing mice. We also thank Y. Morishita and T. Tanda for histological analysis, S. Ehata and J. Nishida for experimental design of the metastasis model, H. Nawa and H. Namba for helping to prepare the Th-EGFP mouse brain, T. Mano for reproducing the image processing pipeline, Tokyo Chemical Industry for the CUBIC chemical library, Olympus Engineering for helping with the microscope design, and Bitplane for instruction in Imaris 8.1.2. This work was supported by grants from AMED-CREST ( AMED/MEXT to H.R.U.) and CREST ( JST/MEXT to H.R.U. and JPMJCR1652 to H.K.); PRESTO from JST ( JPMJPR15F4 to E.A.S.); Brain/MINDS (AMED/MEXT to H.R.U.); the Basic Science and Platform Technology Program for Innovative Biological Medicine ( AMED/MEXT to H.R.U.); the Japanese Initiative for Progress of Research on Infectious Disease for Global Epidemic ( AMED , JP17fm0208023 to M.M. and K. Tainaka); Strategic Research Program from Brain Sciences (AMED , JP18dm0107120 to H.K.); Grant-in-Aid for Challenging Exploratory Research (JSPS KAKENHI grant 16K15124 to K. Tainaka); Grant-in-Aid for Young Scientists (A) (JSPS KAKENHI grant no. 15H05650 to E.A.S.); Grant-in-Aid for Scientific Research (JSPS KAKENHI grant no. 16J05041 to T.C.M.); Grant-in-Aid for Scientific Research (S) (JSPS KAKENHI grant no. 25221004 and 18H05270 to H.R.U. and 26221001 to H.K.); Grant-in-Aid for Scientific Research (B) (JSPS KAKENHI grant no. 18H02105 to K. Tainaka and 18H02540 to T.S. and K. Tainaka); Grants-in-Aid for Scientific Research on Innovative Areas (KAKENHI grant no. 23115006 to H.R.U. and 17H05688 and 18H04543 to K. Tainaka, and 17H06328 to E.A.S.) from MEXT ; Grant-in-Aid from the Naito Science & Engineering Foundation (K. Tainaka); Grant-in-Aid from the Tokyo Biochemical Research Foundation (K. Tainaka); Grant-in-Aid from the Cell Science Research Foundation (K. Tainaka); Grant-in-Aid from the NOVARTIS Foundation (Japan) for the Promotion of Science (K. Tainaka); Grant-in-Aid from the Takeda Science Foundation (H.R.U. and E.A.S.); Grant-in-Aid from the Japan Foundation for Applied Enzymology (E.A.S.); and grant from the Brain Sciences Project of the Center for Novel Science Initiatives of the National Institutes of Natural Sciences ( BS291001 to E.A.S.).
Funding Information:
We thank all of the laboratory members at The University of Tokyo and RIKEN Quantitative Biology Center (QBiC), in particular, K. Yoshida for help with the polynomial regression; S. Shi, G.A. Sunagawa, and R.G. Yamada for statistical analysis; and R. Ohno for housing mice. We also thank Y. Morishita and T. Tanda for histological analysis, S. Ehata and J. Nishida for experimental design of the metastasis model, H. Nawa and H. Namba for helping to prepare the Th-EGFP mouse brain, T. Mano for reproducing the image processing pipeline, Tokyo Chemical Industry for the CUBIC chemical library, Olympus Engineering for helping with the microscope design, and Bitplane for instruction in Imaris 8.1.2. This work was supported by grants from AMED-CREST (AMED/MEXT to H.R.U.) and CREST (JST/MEXT to H.R.U. and JPMJCR1652 to H.K.); PRESTO from JST(JPMJPR15F4 to E.A.S.); Brain/MINDS (AMED/MEXT to H.R.U.); the Basic Science and Platform Technology Program for Innovative Biological Medicine (AMED/MEXT to H.R.U.); the Japanese Initiative for Progress of Research on Infectious Disease for Global Epidemic (AMED, JP17fm0208023 to M.M. and K. Tainaka); Strategic Research Program from Brain Sciences (AMED, JP18dm0107120 to H.K.); Grant-in-Aid for Challenging Exploratory Research (JSPS KAKENHI grant 16K15124 to K. Tainaka); Grant-in-Aid for Young Scientists (A) (JSPS KAKENHI grant no. 15H05650 to E.A.S.); Grant-in-Aid for Scientific Research (JSPS KAKENHI grant no. 16J05041 to T.C.M.); Grant-in-Aid for Scientific Research (S) (JSPS KAKENHI grant no. 25221004 and 18H05270 to H.R.U. and 26221001 to H.K.); Grant-in-Aid for Scientific Research (B) (JSPS KAKENHI grant no. 18H02105 to K. Tainaka and 18H02540 to T.S. and K. Tainaka); Grants-in-Aid for Scientific Research on Innovative Areas (KAKENHI grant no. 23115006 to H.R.U. and 17H05688 and 18H04543 to K. Tainaka, and 17H06328 to E.A.S.) from MEXT; Grant-in-Aid from the Naito Science & Engineering Foundation (K. Tainaka); Grant-in-Aid from the Tokyo Biochemical Research Foundation (K. Tainaka); Grant-in-Aid from the Cell Science Research Foundation (K. Tainaka); Grant-in-Aid from the NOVARTIS Foundation (Japan) for the Promotion of Science (K. Tainaka); Grant-in-Aid from the Takeda Science Foundation (H.R.U. and E.A.S.); Grant-in-Aid from the Japan Foundation for Applied Enzymology (E.A.S.); and grant from the Brain Sciences Project of the Center for Novel Science Initiatives of the National Institutes of Natural Sciences (BS291001 to E.A.S.).
Publisher Copyright:
© 2018 The Author(s)
PY - 2018/8/21
Y1 - 2018/8/21
N2 - 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. Tainaka et al. describe a strategy for developing hydrophilic tissue-clearing reagents based on comprehensive chemical profiling. The strategic integration of optimal chemical cocktails provided a series of CUBIC protocols, which enable the 3D imaging of the mammalian body and large primate and human tissues.
AB - 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. Tainaka et al. describe a strategy for developing hydrophilic tissue-clearing reagents based on comprehensive chemical profiling. The strategic integration of optimal chemical cocktails provided a series of CUBIC protocols, which enable the 3D imaging of the mammalian body and large primate and human tissues.
KW - chemistry in tissue clearing
KW - comprehensive chemical profiling
KW - high-throughput chemical screening
KW - hydrophilic reagents
KW - three-dimensional imaging
KW - virtual multiplex imaging
UR - http://www.scopus.com/inward/record.url?scp=85051499044&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85051499044&partnerID=8YFLogxK
U2 - 10.1016/j.celrep.2018.07.056
DO - 10.1016/j.celrep.2018.07.056
M3 - Article
C2 - 30134179
AN - SCOPUS:85051499044
SN - 2211-1247
VL - 24
SP - 2196-2210.e9
JO - Cell Reports
JF - Cell Reports
IS - 8
ER -