Revealing intact neuronal circuitry in centimeter-sized formalin-fixed paraffin-embedded brain

Ya-Hui Lin; Li-Wen Wang; Yen-Hui Chen; Yi-Chieh Chan; Shang-Hsiu Hu; Sheng-Yan Wu; Chi-Shiun Chiang; Guan-Jie Huang; Shang-Da Yang; Shi-Wei Chu; Kuo-Chuan Wang; Chin-Hsien Lin; Pei-Hsin Huang; Hwai-Jong Cheng; Bi-Chang Chen; Li-An Chu

doi:10.7554/eLife.93212

eLife (May 2024)

Revealing intact neuronal circuitry in centimeter-sized formalin-fixed paraffin-embedded brain

Ya-Hui Lin,
Li-Wen Wang,
Yen-Hui Chen,
Yi-Chieh Chan,
Shang-Hsiu Hu,
Sheng-Yan Wu,
Chi-Shiun Chiang,
Guan-Jie Huang,
Shang-Da Yang,
Shi-Wei Chu,
Kuo-Chuan Wang,
Chin-Hsien Lin,
Pei-Hsin Huang,
Hwai-Jong Cheng,
Bi-Chang Chen,
Li-An Chu

Affiliations

Ya-Hui Lin: ORCiD; Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu, Taiwan; Brain Research Center, National Tsing Hua University, Hsinchu, Taiwan
Li-Wen Wang: Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu, Taiwan; Brain Research Center, National Tsing Hua University, Hsinchu, Taiwan
Yen-Hui Chen: Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
Yi-Chieh Chan: Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu, Taiwan
Shang-Hsiu Hu: Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu, Taiwan
Sheng-Yan Wu: Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu, Taiwan
Chi-Shiun Chiang: ORCiD; Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu, Taiwan
Guan-Jie Huang: Department of Physics, National Taiwan University, Taipei, Taiwan
Shang-Da Yang: Institute of Photonics Technologies, National Tsing Hua University, Hsinchu, Taiwan
Shi-Wei Chu: ORCiD; Department of Physics, National Taiwan University, Taipei, Taiwan
Kuo-Chuan Wang: Department of Neurosurgery, National Taiwan University Hospital, Taipei, Taiwan
Chin-Hsien Lin: Department of Neurosurgery, National Taiwan University Hospital, Taipei, Taiwan
Pei-Hsin Huang: Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan
Hwai-Jong Cheng: Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
Bi-Chang Chen: Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
Li-An Chu: ORCiD; Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu, Taiwan; Brain Research Center, National Tsing Hua University, Hsinchu, Taiwan

DOI: https://doi.org/10.7554/eLife.93212
Journal volume & issue: Vol. 13

Abstract

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Tissue-clearing and labeling techniques have revolutionized brain-wide imaging and analysis, yet their application to clinical formalin-fixed paraffin-embedded (FFPE) blocks remains challenging. We introduce HIF-Clear, a novel method for efficiently clearing and labeling centimeter-thick FFPE specimens using elevated temperature and concentrated detergents. HIF-Clear with multi-round immunolabeling reveals neuron circuitry regulating multiple neurotransmitter systems in a whole FFPE mouse brain and is able to be used as the evaluation of disease treatment efficiency. HIF-Clear also supports expansion microscopy and can be performed on a non-sectioned 15-year-old FFPE specimen, as well as a 3-month formalin-fixed mouse brain. Thus, HIF-Clear represents a feasible approach for researching archived FFPE specimens for future neuroscientific and 3D neuropathological analyses.

Published in eLife

ISSN: 2050-084X (Online)
Publisher: eLife Sciences Publications Ltd
Country of publisher: United Kingdom
LCC subjects: Medicine; Science: Biology (General)
Website: https://elifesciences.org

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