Journal Article

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

van Galen, Peter, Olive, Jessica F., Bizuayehu, Amanuel, Goreczny, Gregory J., Guo, Qiuchen, Maynard, Adam G., McAllister, Sandra S., Spasic, Milos

2022

Overview

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. DNA barcoding methods for the analysis of clonal heterogeneity in cancer have been limited in terms of throughput and practical requirements. Here, the authors develop SunCatcher, a rapid and sensitive barcoding approach for live single-cell clonal evolution analysis, and use this method to study breast cancer cell populations.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 13 / 631/1647/1407/2181 / 631/67/1347 / 631/67/2329 / 631/80 / Breast cancer / Cancer research / Cell Line / Clonal Evolution - genetics / Clone Cells / Cloning / Evolution / Experimentation / Functional analysis / Gene sequencing / Heterogeneity / High-Throughput Nucleotide Sequencing - methods / Humanities and Social Sciences / Metastases / multidisciplinary / Neoplasms / Next-generation sequencing / Population studies / Populations / Real-Time Polymerase Chain Reaction / Science / Science (multidisciplinary) / Tumor cell lines / Tumors