Clonal barcoding with qPCR detection enables live cell functional analyses for cancer research

Qiuchen Guo, Milos Spasic, Adam G. Maynard, Gregory J. Goreczny, Amanuel Bizuayehu, Jessica F. Olive, Peter Galen and Sandra S. McAllister ()
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Qiuchen Guo: Brigham and Women’s Hospital
Milos Spasic: Brigham and Women’s Hospital
Adam G. Maynard: Harvard Medical School
Gregory J. Goreczny: Brigham and Women’s Hospital
Amanuel Bizuayehu: Brigham and Women’s Hospital
Jessica F. Olive: Brigham and Women’s Hospital
Peter Galen: Brigham and Women’s Hospital
Sandra S. McAllister: Brigham and Women’s Hospital

Nature Communications, 2022, vol. 13, issue 1, 1-15

Abstract: Abstract Single-cell analysis methods are valuable tools; however, current approaches do not easily enable live cell retrieval. That is a particular issue when further study of cells that were eliminated during experimentation could provide critical information. We report a clonal molecular barcoding method, called SunCatcher, that enables longitudinal tracking and live cell functional analysis. From complex cell populations, we generate single cell-derived clonal populations, infect each with a unique molecular barcode, and retain stocks of individual barcoded clones (BCs). We develop quantitative PCR-based and next-generation sequencing methods that we employ to identify and quantify BCs in vitro and in vivo. We apply SunCatcher to various breast cancer cell lines and combine respective BCs to create versions of the original cell lines. While the heterogeneous BC pools reproduce their original parental cell line proliferation and tumor progression rates, individual BCs are phenotypically and functionally diverse. Early spontaneous metastases can also be identified and quantified. SunCatcher thus provides a rapid and sensitive approach for studying live single-cell clones and clonal evolution, and performing functional analyses.

Date: 2022
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DOI: 10.1038/s41467-022-31536-5

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