Isolation of specific cell types, including pluripotent stem cell (PSC)-derived populations,
is frequently accomplished using cell surface antigens expressed by the cells of interest.
However, specific antigens for many cell types have not been identified, making their
isolation difficult. Here, we describe an efficient method for purifying cells based
on endogenous miRNA activity. We designed synthetic mRNAs encoding a fluorescent protein
tagged with sequences targeted by miRNAs expressed by the cells of interest. These
miRNA switches control their translation levels by sensing miRNA activities. Several
miRNA switches (miR-1-, miR-208a-, and miR-499a-5p-switches) efficiently purified
cardiomyocytes differentiated from human PSCs, and switches encoding the apoptosis
inducer Bim enriched for cardiomyocytes without cell sorting. This approach is generally
applicable, as miR-126-, miR-122-5p-, and miR-375-switches purified endothelial cells,
hepatocytes, and insulin-producing cells differentiated from hPSCs, respectively.
Thus, miRNA switches can purify cell populations for which other isolation strategies
are unavailable.