High-content, targeted RNA-seq screening in organoids for drug discovery in colorectal cancer

We present TORNADO-seq —a high-throughput, a high-content drug discovery platform that for the first time uses next-generation sequencing (NGS) based, targeted RNA-seq in organoids monitoring the expression of 206 genes for the evaluation of complex mixtures of cellular phenotypes. TORNADO-seq is a fast, highly-reproducible, time- and cost-effective (5$ per sample including sequencing cost) method that we used to find drugs that enrich for differentiated cell phenotypes in intestinal organoids. These drugs are highly efficacious against cancer compared to wild type organoids and may therefore become promising candidates in CRC treatment. Further, TORNADO-seq facilitated in-depth insight on the mode of action of these drugs. Overall design: We have screened 320 compounds from a library of FDA-approved drugs on WT and AKP (APC, KRAS, p53) mutant intestinal organoids in 96-well plate format. 2-4 biological replicates were used, and 1 or 2 days treatment duration.