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

Sarah M. Hücker, Tobias Fehlmann, Christian Werno, Kathrin Weidele, Florian Lüke, Anke Schlenska-Lange, Christoph A. Klein, Andreas Keller and Stefan Kirsch ()
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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
Anke Schlenska-Lange: Hospital Barmherzige Brüder
Christoph A. Klein: Division of Personalized Tumor Therapy, Fraunhofer-Institute for Toxicology and Experimental Medicine
Andreas Keller: Chair for Clinical Bioinformatics, Saarland University
Stefan Kirsch: Division of Personalized Tumor Therapy, Fraunhofer-Institute for Toxicology and Experimental Medicine

Nature Communications, 2021, vol. 12, issue 1, 1-13

Abstract: 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.

Date: 2021
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DOI: 10.1038/s41467-021-24611-w

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