Comprehensive microRNA analysis across genome-edited colorectal cancer organoid models reveals miR-24 as a candidate regulator of cell survival

Colorectal cancer (CRC) is the third most diagnosed cancer and the second leading cause of cancer-related death worldwide Unique mutational combinations can result in distinct changes to gene regulatory mechanisms leading to variability in the efficacy of available therapeutics. To work toward novel therapeutic strategies, it is important to understand the mechanisms by which unique combinations of mutations affect gene regulatory mechanisms. To that end, in this study, we generated RNA- and small RNA-seq data from Apc (A; n=3), Apc/Kras/p53 (AKP; n=1), B-catenin (B; n=5), B-catenin/Kras/p53 (BKP; n=1), Kras/Rspo3/p53 (KRP; n=2), Kras/Rspo3/p53/Smad4 (KRPS; n=4), Kras/Rspo3/Smad4 (KRS; n=3), Rspo3 (R; n=2) mutant mouse enteroids, and wild-type (WT; n=2) controls. From this analysis, we found that miR-24-3p is upregulated master miRNA regulator across mutational contexts. Functional studies identified miR-24-3p as a regulator of cell survival. Utilizing RNA- and leChRO-seq from HCT116 cells treated with a miR-24-3p inhibitor (n=3) or scramble control (n=3), we identified HMOX1 and PRSS8 as candidate miR-24-3p targets subject to post-transcriptional regulation by miR-24-3p. RNA- and small RNA-seq comparison between genetically modified mouse enteroid models and WT control. RNA- and ChRO-seq comparison between HCT116 cells treated with a miR-24-3p inhibitor or scramble control.