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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,C. Chiang,Guan-Jie Huang,Shang-Da Yang,S. Chu,Kuo-Chuan Wang,Chin-Hsien Lin,Pei-Hsin Huang,Hwai-Jong Cheng,Bi-Chang Chen,L. Chu

Published 2024 in bioRxiv

ABSTRACT

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.

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