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

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

Elife. 2024 May 22:13:RP93212. doi: 10.7554/eLife.93212.

Authors

Ya-Hui Lin^{1

2}, Li-Wen Wang^{1

2}, Yen-Hui Chen³, Yi-Chieh Chan¹, Shang-Hsiu Hu¹, Sheng-Yan Wu¹, Chi-Shiun Chiang¹, Guan-Jie Huang⁴, Shang-Da Yang⁵, Shi-Wei Chu⁴, Kuo-Chuan Wang⁶, Chin-Hsien Lin⁶, Pei-Hsin Huang⁷, Hwai-Jong Cheng⁸, Bi-Chang Chen⁹, Li-An Chu^{1

2}

Affiliations

¹ Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu, Taiwan.
² Brain Research Center, National Tsing Hua University, Hsinchu, Taiwan.
³ Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.
⁴ Department of Physics, National Taiwan University, Taipei, Taiwan.
⁵ Institute of Photonics Technologies, National Tsing Hua University, Hsinchu, Taiwan.
⁶ Department of Neurosurgery, National Taiwan University Hospital, Taipei, Taiwan.
⁷ Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan.
⁸ Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.
⁹ Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan.

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.

Keywords: FFPE; archived tissues; human; mouse; multiplexed staining; neuroscience; tissue clearing; whole brain analysis; whole mouse brain imaging.

MeSH terms

Animals
Brain*
Fixatives / chemistry
Formaldehyde*
Mice
Neurons* / physiology
Paraffin Embedding* / methods
Tissue Fixation* / methods

Associated data

Dryad/10.5061/dryad.prr4xgxv7

Abstract

MeSH terms

Associated data

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