A multifunctional tracking approach to study clonal heterogeneity in leukemia by flow cytometry and scRNA-seq

Acute myeloid leukemia (AML) is characterized by clonal heterogeneity, the main cause of treatment failure and relapse. Sequencing is commonly used for studying clonal composition; however, this impairs the functional validation of new findings. Therefore, we envisioned a system that combines scRNA-seq with flow cytometric clonal tracking and additionally enables the re-isolation of viable clones for further characterization. We developed a lentiviral gene marking strategy that labels leukemic cells with color codes and transcribed DNA-barcodes compatible with single-cell sequencing. Here, we could show the reliable detection of up to 48 color codes by flow cytometry. Populations of different color codes were tracked in vitro allowing the visualization of competitive growth behaviors. Furthermore, we could prove the specificity of our barcode detection by scRNA-seq. This project aims to delineate clonal competition under naïve conditions and upon therapeutic pressure in vivo. By correlating clonal behavior to transcriptional and (epi-) genetic profiles, we envision the identification of disease-relevant features and their functional validation for improved intervention strategies.

Publication History

Article published online:
17 May 2022