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.93212.4

NeuroscienceeLifeMay 22, 2024

Peer-reviewed journal article

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

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

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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