Rapid identification of human mast cell degranulation regulators using functional genomics coupled to high-resolution confocal microscopy

Targeted functional genomics represents a powerful approach for studying gene function in vivo and in vitro. However, its application to gene expression studies in human mast cells has been hampered by low yields of human mast cell cultures and their poor transfection efficiency. We developed an imaging system in which mast cell degranulation can be visualized in single cells subjected to shRNA knockdown or CRISPR-Cas 9 gene editing. By using high resolution confocal microscopy and a fluorochrome-labeled avidin probe, one can directly assess the suppression of functional responses, i.e. degranulation, in single human mast cells. The elimination of a drug or marker selection step avoids the use of potentially toxic treatment procedures and the short hands-on time of the functional analysis step enables the high-throughput screening of shRNA or CRISPR-Cas9 constructs to identify genes that regulate human mast cell degranulation. The ability to analyse single cells significantly reduces the total number of cells required, and allows for the parallel visualization of the degranulation profile of both edited and non-edited mast cells, offering a consistent internal control not found in other protocols. Moreover, our protocol offers a flexible choice between RNA interference and CRISPR-Cas9 genome editing for perturbation of gene expression using our human mast cell single-cell imaging system. Perturbation of gene expression, acquisition of microscopy data, and image analysis can be completed within 5 days, requiring only standard laboratory equipment and expertise.