High-throughput intracellular biopsy of microRNAs for dissecting the temporal dynamics of cellular heterogeneity

• Published in: Science advances 2020-06, Vol.6 (24), p.eaba4971-eaba4971
• Main Authors: Wang, Zixun, Qi, Lin, Yang, Yang, Lu, Mingxing, Xie, Kai, Zhao, Xi, Cheung, Elvis Hung Chi, Wang, Yuan, Jiang, Xuezhen, Zhang, Wenjun, Huang, Linfeng, Wang, Xin, Shi, Peng
• Format: Article
• Language: English
• Subjects: Applied Sciences and Engineering; Biopsy; Gene Expression Profiling; Gene Expression Regulation; Genetics; MicroRNAs - metabolism; SciAdv r-articles; Transcriptome
• ISSN: 2375-2548; 2375-2548
• DOI: 10.1126/sciadv.aba4971

The capability to analyze small RNAs responsible for post-transcriptional regulation of genes expression is essential for characterizing cellular phenotypes. Here, we describe an intracellular biopsy technique (inCell-Biopsy) for fast, multiplexed, and highly sensitive profiling of microRNAs (miRNAs). The technique uses an array of diamond nanoneedles that are functionalized with size-dependent RNA binding proteins, working as "fishing rods" to directly pull miRNAs out of cytoplasm while keeping the cells alive, thus enabling quasi-single-cell miRNA analysis. Each nanoneedle works as a reaction chamber for parallel in situ amplification, visualization, and quantification of miRNAs as low as femtomolar, which is sufficient to detect miRNAs of a single-copy intracellular abundance with specificity to single-nucleotide variation. Using inCell-Biopsy, we analyze the temporal miRNA transcriptome over the differentiation of embryonic stem cells (ESCs). The combinatorial miRNA expression patterns derived by inCell-Biopsy identify emerging cell subpopulations differentiated from ESCs and reveal the dynamic evolution of cellular heterogeneity.