Fluorescent genetic barcoding for cellular multiplex analyses

Hematopoiesis depends on the controlled differentiation of hematopoietic stem cells to mature cells with defined functions. Although each cell population within the hematopoietic hierarchy can be described by phenotypic markers, isolation of marker pure populations does not necessarily result in cells with homogeneous functionality. However, techniques that enable the efficient characterization of cell behavior with high resolution are limited. Although single-cell transplantation assays demand high mouse numbers and workload, sequencing-based fate tracking techniques require the destruction of the host cell, substantial financial resources, and bioinformatics expertise and suffer from a delay between sample acquisition and data interpretation. To make analyses more efficient, several laboratories recently developed flow cytometry-driven, fluorescence-based multiplexing approaches that enable parallel analysis of longitudinal behavior from multiple clonally derived cells or polyclonal populations. Although these fluorescent genetic barcoding systems are still in their infancy, their power lies in the use of retroviral vectors for gene marking of multiple populations with unique fluorescent color codes. Tracing of color-coded cells by flow cytometry guarantees the accessibility of information on population behavior in real time and at low cost, supports the prospective isolation of cells for downstream analyses, and can be applied to cell line models as well as to human- and animal-derived primary cells. Here, we discuss recent progress in the emerging field of fluorescent genetic barcoding for longitudinal multiplex cell tracking in biomedical research and how this technique will help to uncover mechanisms regulating cell behavior with clonal resolution in a reduced number of experimental samples.