Citation: Xiaowen Cao, Yuheng Zhu, Siyue Fan, Feng Chen, Yongxi Zhao. Accurate counting of RNA in tissues with highly denoising amplified imaging[J]. Chinese Chemical Letters, ;2025, 36(12): 111091. doi: 10.1016/j.cclet.2025.111091 shu

Accurate counting of RNA in tissues with highly denoising amplified imaging

Xiaowen Cao ^a ,
Yuheng Zhu ^a ,
Siyue Fan ^a ,
Feng Chen ^{a, *,} ,
Yongxi Zhao ^{a, b, *,}

a.
Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
b.
Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China

fengchencf@mail.xjtu.edu.cn

yxzhao@mail.xjtu.edu.cn

Received Date: 8 September 2024
Revised Date: 6 February 2025
Accepted Date: 13 March 2025
Available Online: 15 March 2025

Figures(5)

Characterization of the distribution and accurate counting of RNA molecules in the context of tissues is necessary to understand their complexity and heterogeneity. Single-molecule fluorescence in situ hybridization reveals the abundance and distribution of RNA and resolves different cell types in complex tissues. Especially, off-target binding and nonspecific adsorption of probes are prone to producing nonspecific amplification. Herein, we present highly de-noising amplified imaging, which leverages a site-specific cleavage-amplifying design to achieve accurate counting of RNA in tissues. Our method avoids adding probe as primer, decreases nonspecific spots of single cells from 7 to nearly zero, and enables RNA imaging in uncleared tissue sections with nearly zero noise. We demonstrate the efficacy of this method on various thickness of mouse tissue sections. We envision this approach will serve as a tool to revealing the information content from patient samples for biomedical purpose.
- Nucleic acid amplification,
- RNA endonuclease,
- RNA counting,
- Single-cell imaging,
- Tissue sections
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