Abstract 1474: Genome edited colorectal cancer organoid models reveal distinct microRNA activity patterns across different mutation profiles

Abstract Colorectal cancer (CRC) is the third most common cancer and second leading cause of cancer-related deaths worldwide. DNA mutations drive colon tumor formation by disrupting gene regulatory mechanisms that facilitate cell survival and growth. Distinct combinations of mutations can result in unique changes to these gene regulatory mechanisms leading to variability in responses to available therapeutics. MicroRNAs (miRNAs) are important regulators of gene expression in CRC and it is known that their expression can be altered by oncogenic mutations. However, it is unknown how distinct combinations of CRC-risk mutations differentially affect the regulation and expression of miRNAs. We hypothesize that some miRNAs will exhibit strong genotype-dependent changes in CRC whereas others will be altered irrespective of genotype. Utilizing sequencing data from The Cancer Genome Atlas (TCGA) and cutting-edge intestinal organoid (enteroid) models with different combinations of oncogenic mutations that commonly occur in CRC, we identified several distinct patterns of genotype-dependent miRNA expression. We also found a suite of miRNAs that are up-regulated in a mutation-independent manner. Among these, we demonstrated that miR-24-3p is a candidate master regulator of genes that are down-regulated in all mutational-contexts. RT-qPCR for miR-24-3p in genetically modified human colonoids with different combinations of oncogenic mutations further supports that miR-24-3p is elevated across various mutational contexts. Functional studies in the HCT116 cell line revealed that miR-24-3p controls the number of metabolically active, viable cells by regulating apoptosis but not proliferation. Moreover, follow-up ex vivo studies in mouse enteroids confirmed that miR-24 controls intestinal cell survival. To identify candidate gene targets that mediate the function of miR-24-3p, I performed an RNA-sequencing (RNA-seq) analysis and identified HMOX1 and PRSS8 as top candidate miR-24-3p targets. These findings suggest that miR-24-3p is a genotype-independent regulator of tumor cell apoptosis in CRC and merits further investigation. Overall, our findings provide a novel perspective on approaches for precision medicine in CRC. Citation Format: Jonathan W. Villanueva, Lawrence Kwong, Teng Han, Salvador Alonso Martinez, Fong Cheng Pan, Michael T. Shanahan, Matt Kanke, Shuibing Chen, Lukas E. Dow, Charles G. Danko, Praveen Sethupathy. Genome edited colorectal cancer organoid models reveal distinct microRNA activity patterns across different mutation profiles [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1474.