A multi-kingdom genetic barcoding system for precise target clone isolation

Pillar 4
Functional Genomics & Structure-Function of VOCs

Clonal heterogeneity underlies diverse biological processes, including viral infection, cancer progression, cell differentiation, and microbial evolution. In the concept of cell tagging, unique DNA barcodes are introduced to individual cells. The barcoded cells can be subjected to a given assay (like virus infection assay) to test if any specific clones exist to be preferred for a target biological event (like virus infection). However, isolating a target clone from a complex cell population before it displays a specific outcome remains challenging. If such a technology exists, we can interrogate the cellular and molecular states that prevent and accelerate cells to enter a specific state. Using CRISPR-Cas9 genome editing technology, we developed a new time-machine-like system, CloneSelect. In CloneSelect, cells are first barcoded and propagated so their subpopulation can be subjected to a given experiment. A clone that shows a phenotype or genotype of interest at a given time can then be isolated from the initial or subsequent cell pools stored throughout the experimental time course. This novel platform provides many new ways of analyzing viral infection, cancer, cell differentiation, and development in human and other mammalian systems, as well as diverse mechanisms in yeast and bacterial systems.

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