GSE110784
miRNA expression profiles of HeLa-Cas9 and NCI-N87 cells
MicroRNAs (miRNAs) play an important role in the regulation of gene expression and are often dysregulated in disease. The recent development of the CRISPR-Cas9 gene-editing system, composed of the Cas9 nuclease in complex with a single guide RNA (sgRNA), allows researchers to direct DNA cleavage at a predetermined site and to conduct genome-scale knockout screens. To determine the functional role of miRNAs in cancer, we designed and constructed a library of 7,382 sgRNAs to target 85% of the 1,881 annotated human miRNA stem-loops. We then examined the role of miRNAs in HeLa cell fitness by monitoring the change in frequency of each sgRNA over time. We identified 44 pro-proliferative miRNAs from two replicate experiments, including miR-31, a known cervical cancer overexpressing miRNA that enhances HeLa cell proliferation. We also examined the role of miRNAs in NCI-N87 gastric cancer cells and identified 10 pro-fitness and 10 anti-fitness miRNAs. In both screens, many of the pro-fitness miRNAs identified are overexpressed in tumors cervical tumors for HeLa or gastric tumors for NCI-N87. In summary, we present a CRISPR miRNA-targeted screen which was able to identify both known and novel fitness-associated miRNAs in the HeLa and NCI-N87 cell lines. Overall design: The miRNA expression profile of NCI-N87 gastric cancer cells was determined by high throughput miRNA sequencing (NCI-N87_miR-seq). To determine the miRNA expression profile of the clonal HeLa-Cas9 cell line, we determined the miRNA expression in HeLa-Cas9 cells 9 days after transduction with the LX-miR library for two biological replicates (HeLa_1D7_miR-seq and HeLa_2D7_miR-seq). To examine the impact of doxycycline treatment on miRNA expression, we also profiled the miRNA expression in HeLa-Cas9 cells with (HeLa_1D22G1_miR-seq) and without (HeLa_1D22md_miR-seq) doxycycline treatment.