Arrayed Molecular Barcoding of Leukemic Stem Cells.

Functional screens on cancer cells using compound or protein libraries are usually performed in vitro. However, to assess the effects on leukemia stem cells (LSCs) in a screening setting, methodologies that allow for a high-throughput in vivo readout of leukemia-initiating activity are needed. One experimental approach to solve this issue is to genetically label, also referred to as "barcoding," the leukemia cells in an arrayed format prior to exposing them to separate experimental conditions. The cells can then be pooled and injected into mice for competitive readout of leukemia-initiating activity. Here, we describe a procedure for combining lentiviral arrayed molecular barcoding of leukemia cells with next-generation sequencing, to enable screens on leukemia cells ex vivo followed by an in vivo competitive readout of LSC function. This methodology can also be applied to other model systems in which a competitive in vivo readout of cells is needed.