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

• Published in: eLife Vol. 13
• Main Authors: Lin, Ya-Hui, Wang, Li-Wen, Chen, Yen-Hui, Chan, Yi-Chieh, Hu, Shang-Hsiu, Wu, Sheng-Yan, Chiang, Chi-Shiun, Huang, Guan-Jie, Yang, Shang-Da, Chu, Shi-Wei, Wang, Kuo-Chuan, Lin, Chin-Hsien, Huang, Pei-Hsin, Cheng, Hwai-Jong, Chen, Bi-Chang, Chu, Li-An
• Format: Journal Article
• Language: English
• Published: 22.05.2024
• ISSN: 2050-084X; 2050-084X
• DOI: 10.7554/eLife.93212.4

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.