Computer-aided design of reversible hybridization chain reaction (CAD-HCR) enables multiplexed single-cell spatial proteomics imaging

Xiaohao Liu; Dongsheng Mao; Yuchen Song; Liucun Zhu; Albertina N Isak; Cuicui Lu; Guoli Deng; Feng Chen; Fenyong Sun; Yu Yang; Xiaoli Zhu; Weihong Tan

doi:10.1126/sciadv.abk0133

Computer-aided design of reversible hybridization chain reaction (CAD-HCR) enables multiplexed single-cell spatial proteomics imaging

Sci Adv. 2022 Jan 14;8(2):eabk0133. doi: 10.1126/sciadv.abk0133. Epub 2022 Jan 14.

Authors

Xiaohao Liu^{1

2}, Dongsheng Mao^{2

3}, Yuchen Song², Liucun Zhu², Albertina N Isak², Cuicui Lu², Guoli Deng², Feng Chen¹, Fenyong Sun¹, Yu Yang³, Xiaoli Zhu^{1

2}, Weihong Tan^{3

4

5}

Affiliations

¹ Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200072, China.
² Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China.
³ Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
⁴ The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China.
⁵ Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China.

Abstract

In situ spatial proteomics analysis of a single cell has not been achieved yet, mainly because of insufficient throughput and sensitivity of current techniques. Recent progress on immuno-nucleic acid amplification technology presents tremendous opportunities to address this issue. Here, we report an innovative hybridization chain reaction (HCR) technique that involves computer-aided design (CAD) and reversible assembly. CAD enables highly multiplexed HCR with a sequence database that can work in parallel, while reversible assembly enables the switching of HCR between a working state and a resting state. Thus, CAD-HCR has been successfully adopted for single-cell spatial proteomics analysis. The fluorescence signal of CAD-HCR is comparable with conventional immunofluorescence, and it is positively correlated with the abundance of target proteins, which is beneficial for the visualization of proteins. The method developed here expands the toolbox of single-cell analysis and proteomics studies, as well as the performance and application of HCR.