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

Zixun Wang; Lin Qi; Yang Yang; Mingxing Lu; Kai Xie; Xi Zhao; Elvis Hung Chi Cheung; Yuan Wang; Xuezhen Jiang; Wenjun Zhang; Linfeng Huang; Xin Wang; Peng Shi

doi:10.1126/sciadv.aba4971

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

Zixun Wang (Co-first Author), Lin Qi (Co-first Author), Yang Yang (Co-first Author), Mingxing Lu, Kai Xie, Xi Zhao, Elvis Hung Chi Cheung, Yuan Wang, Xuezhen Jiang, Wenjun Zhang^*, Linfeng Huang^*, Xin Wang^*, Peng Shi^*

^*Corresponding author for this work

Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

30 Citations (Scopus)

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Abstract

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 inCellBiopsy identify emerging cell subpopulations differentiated from ESCs and reveal the dynamic evolution of cellular heterogeneity.

Original language	English
Article number	eaba4971
Journal	Science Advances
Volume	6
Issue number	24
Online published	10 Jun 2020
DOIs	https://doi.org/10.1126/sciadv.aba4971
Publication status	Published - 10 Jun 2020

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This full text is made available under CC-BY-NC 4.0. https://creativecommons.org/licenses/by-nc/4.0/

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title = "High-throughput intracellular biopsy of microRNAs for dissecting the temporal dynamics of cellular heterogeneity",

abstract = "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 inCellBiopsy identify emerging cell subpopulations differentiated from ESCs and reveal the dynamic evolution of cellular heterogeneity.",

author = "Zixun Wang and Lin Qi and Yang Yang and Mingxing Lu and Kai Xie and Xi Zhao and Cheung, {Elvis Hung Chi} and Yuan Wang and Xuezhen Jiang and Wenjun Zhang and Linfeng Huang and Xin Wang and Peng Shi",

year = "2020",

month = jun,

day = "10",

doi = "10.1126/sciadv.aba4971",

language = "English",

volume = "6",

journal = "Science Advances",

issn = "2375-2548",

publisher = "American Association for the Advancement of Science",

number = "24",

}

High-throughput intracellular biopsy of microRNAs for dissecting the temporal dynamics of cellular heterogeneity. / Wang, Zixun (Co-first Author); Qi, Lin (Co-first Author); Yang, Yang (Co-first Author) et al.
In: Science Advances, Vol. 6, No. 24, eaba4971, 10.06.2020.

Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

TY - JOUR

T1 - High-throughput intracellular biopsy of microRNAs for dissecting the temporal dynamics of cellular heterogeneity

AU - Wang, Zixun

AU - Qi, Lin

AU - Yang, Yang

AU - Lu, Mingxing

AU - Xie, Kai

AU - Zhao, Xi

AU - Cheung, Elvis Hung Chi

AU - Wang, Yuan

AU - Jiang, Xuezhen

AU - Zhang, Wenjun

AU - Huang, Linfeng

AU - Wang, Xin

AU - Shi, Peng

PY - 2020/6/10

Y1 - 2020/6/10

N2 - 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 inCellBiopsy identify emerging cell subpopulations differentiated from ESCs and reveal the dynamic evolution of cellular heterogeneity.

AB - 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 inCellBiopsy identify emerging cell subpopulations differentiated from ESCs and reveal the dynamic evolution of cellular heterogeneity.

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JO - Science Advances

JF - Science Advances

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

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GRF: Dissecting Age-dependent Molecular Heterogeneity of Colorectal Cancer and Establishing a Probabilistic Model for Robust Prediction of High-risk Young-onset Colorectal Cancer Patients

HMRF: The Development of Upconversion-based Wireless Optogenetics as an All-optical Therapeutic Strategy to Study and Treat Parkinson's Disease

GRF: Multi-omic Molecular Subtyping of Ovarian High-grade Serous Carcinoma and Multidimensional Network Inference for Dissecting the Mesenchymal Subtype Specific Regulatory Mechanisms

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

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GRF: Dissecting Age-dependent Molecular Heterogeneity of Colorectal Cancer and Establishing a Probabilistic Model for Robust Prediction of High-risk Young-onset Colorectal Cancer Patients

HMRF: The Development of Upconversion-based Wireless Optogenetics as an All-optical Therapeutic Strategy to Study and Treat Parkinson's Disease

GRF: Multi-omic Molecular Subtyping of Ovarian High-grade Serous Carcinoma and Multidimensional Network Inference for Dissecting the Mesenchymal Subtype Specific Regulatory Mechanisms

Cite this