Highly efficient and robust π-FISH rainbow for multiplexed in situ detection of diverse biomolecules

Yingfeng Tao, Xiaoliu Zhou, Leqiang Sun, Da Lin, Huaiyuan Cai, Xi Chen, Wei Zhou, Bing Yang, Zhe Hu, Jing Yu, Jing Zhang, Xiaoqing Yang, Fang Yang, Bang Shen, Wenbao Qi, Zhenfang Fu, Jinxia Dai () and Gang Cao ()
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Yingfeng Tao: Huazhong Agricultural University
Xiaoliu Zhou: Huazhong Agricultural University
Leqiang Sun: Huazhong Agricultural University
Da Lin: Huazhong Agricultural University
Huaiyuan Cai: Huazhong Agricultural University
Xi Chen: Huazhong Agricultural University
Wei Zhou: Huazhong Agricultural University
Bing Yang: Huazhong Agricultural University
Zhe Hu: Huazhong Agricultural University
Jing Yu: Huazhong University of Science and Technology
Jing Zhang: Huazhong University of Science and Technology
Xiaoqing Yang: Hospital of Huazhong Agricultural University
Fang Yang: Huazhong Agricultural University
Bang Shen: Huazhong Agricultural University
Wenbao Qi: South China Agricultural University
Zhenfang Fu: University of Georgia
Jinxia Dai: Huazhong Agricultural University
Gang Cao: Huazhong Agricultural University

Nature Communications, 2023, vol. 14, issue 1, 1-15

Abstract: Abstract In the unprecedented single-cell sequencing and spatial multiomics era of biology, fluorescence in situ hybridization (FISH) technologies with higher sensitivity and robustness, especially for detecting short RNAs and other biomolecules, are greatly desired. Here, we develop the robust multiplex π-FISH rainbow method to detect diverse biomolecules (DNA, RNA, proteins, and neurotransmitters) individually or simultaneously with high efficiency. This versatile method is successfully applied to detect gene expression in different species, from microorganisms to plants and animals. Furthermore, we delineate the landscape of diverse neuron subclusters by decoding the spatial distribution of 21 marker genes via only two rounds of hybridization. Significantly, we combine π-FISH rainbow with hybridization chain reaction to develop π-FISH+ technology for short nucleic acid fragments, such as microRNA and prostate cancer anti-androgen therapy-resistant marker ARV7 splicing variant in circulating tumour cells from patients. Our study provides a robust biomolecule in situ detection technology for spatial multiomics investigation and clinical diagnosis.

Date: 2023
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DOI: 10.1038/s41467-023-36137-4

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