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Single-cell microRNA sequencing method comparison and application to cell lines and circulating lung tumor cells

Author

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  • Sarah M. Hücker

    (Division of Personalized Tumor Therapy, Fraunhofer-Institute for Toxicology and Experimental Medicine)

  • Tobias Fehlmann

    (Chair for Clinical Bioinformatics, Saarland University)

  • Christian Werno

    (Division of Personalized Tumor Therapy, Fraunhofer-Institute for Toxicology and Experimental Medicine)

  • Kathrin Weidele

    (Division of Personalized Tumor Therapy, Fraunhofer-Institute for Toxicology and Experimental Medicine)

  • Florian Lüke

    (Division of Personalized Tumor Therapy, Fraunhofer-Institute for Toxicology and Experimental Medicine
    University Medical Center Regensburg)

  • Anke Schlenska-Lange

    (Hospital Barmherzige Brüder)

  • Christoph A. Klein

    (Division of Personalized Tumor Therapy, Fraunhofer-Institute for Toxicology and Experimental Medicine
    Experimental Medicine and Therapy Research, University of Regensburg)

  • Andreas Keller

    (Chair for Clinical Bioinformatics, Saarland University
    Center for Bioinformatics, Saarland Informatics Campus
    Stanford University)

  • Stefan Kirsch

    (Division of Personalized Tumor Therapy, Fraunhofer-Institute for Toxicology and Experimental Medicine)

Abstract

Molecular single cell analyses provide insights into physiological and pathological processes. Here, in a stepwise approach, we first evaluate 19 protocols for single cell small RNA sequencing on MCF7 cells spiked with 1 pg of 1,006 miRNAs. Second, we analyze MCF7 single cell equivalents of the eight best protocols. Third, we sequence single cells from eight different cell lines and 67 circulating tumor cells (CTCs) from seven SCLC patients. Altogether, we analyze 244 different samples. We observe high reproducibility within protocols and reads covered a broad spectrum of RNAs. For the 67 CTCs, we detect a median of 68 miRNAs, with 10 miRNAs being expressed in 90% of tested cells. Enrichment analysis suggested the lung as the most likely organ of origin and enrichment of cancer-related categories. Even the identification of non-annotated candidate miRNAs was feasible, underlining the potential of single cell small RNA sequencing.

Suggested Citation

  • Sarah M. Hücker & Tobias Fehlmann & Christian Werno & Kathrin Weidele & Florian Lüke & Anke Schlenska-Lange & Christoph A. Klein & Andreas Keller & Stefan Kirsch, 2021. "Single-cell microRNA sequencing method comparison and application to cell lines and circulating lung tumor cells," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-24611-w
    DOI: 10.1038/s41467-021-24611-w
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    References listed on IDEAS

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    1. Carsten Sticht & Carolina De La Torre & Alisha Parveen & Norbert Gretz, 2018. "miRWalk: An online resource for prediction of microRNA binding sites," PLOS ONE, Public Library of Science, vol. 13(10), pages 1-6, October.
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    Cited by:

    1. Weina Xu & Jinyi Liu & Huan Qi & Ruolin Si & Zhiguang Zhao & Zhiju Tao & Yuchuan Bai & Shipeng Hu & Xiaohan Sun & Yulin Cong & Haoye Zhang & Duchangjiang Fan & Long Xiao & Yangyang Wang & Yongbin Li &, 2024. "A lineage-resolved cartography of microRNA promoter activity in C. elegans empowers multidimensional developmental analysis," Nature Communications, Nature, vol. 15(1), pages 1-23, December.

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