miR-29 mimic and inhibitor expression in the clear cell renal cell carcinoma cell lines 786-O, A-498 and ACHN

The goal of this study was to investigate the regulatory events underlying post-transcriptional changes in gene expression in cancer. We observed that the miR-29 regulon had reccurently increased mRNA stability across multiple cancer types and hypothesized that its down-regulation is responsible at least in part for alterations in the cancer transcriptome. To verify if restoring miR-29 activity can partially reverse these changes, we expressed a miR-29 mimic in the 786-O and A-498 clear cell renal cell carcinoma (ccRCC) lines and performed RNA-sequencing on extracted RNA. We computed differential gene expression in the cell lines expressing the miR-29 mimic, compared to the control sample. We observed that expression of miR-29 mimic partially shifts the transcriptome of cells toward a normal cell state, primarily by down-regulating the majority of genes that are up-regulated in ccRCC tumors, most of which are also miR-29 targets. We observed opposite trends when expressing a miR-29 inhibitor in the ACHN ccRCC cell line. The results suggest that miR-29 downregulation is responsible for changes in the mRNA stability of a considerable number of genes in ccRCC, which can be partially rescued when miR-29 activity is restored. Overall design: RNA-seq of 786-O and A-498 cells expressing a miR-29 mimic or a miRNA mimic control, and ACHN cells expressing a miR-29 inhibitor or miRNA inhibitor control, performed using Illumina NovaSeq 6000 S4 PE100