GSE193402
Comparative RNA sequencing identifies superior cytocidal mechanisms of imatinib over rapamycin in UMB1949 renal angiomyolipoma cells
We report results of RNA sequencing analysis of serum starved UMB1949 renal angiomyolipoma (AML) cells comparatively treated for 24hrs at 37C and 5% CO2 with rapamycin (0.05uM and 1uM) and tyrosine kinase inhibitor (TKI) imatinib (1uM and 10uM). Experiments were done in triplicates per drug concentration. This study was performed to investigate the biological mechanisms underlying superior cytocidal capabilities of the TKI over FDA-approved rapamycin by inhibiting receptor tyrosine kinases on mesenchymal tumorigenic cells in Tuberous Sclerosis and Lymphangioleiomyomatosis (LAM) diseases. Total RNA isolates (RIN>8.0) were sequenced on an illumina Novaseq6000 platform at 100 base pairs to a depth of 30 milllion single end reads. Real-Time Analysis was used for base callling converted to fastq format with bcl2fastq2. Pseudoalignment of RNA-seq reads to a kallisto index was created from human reference genome NCBI/GRCh38.p13. Reads were also mapped to this reference genome using STAR (2.5.2b) and featureCounts (v1.5.0-p3) for results comparison. Differential expression was resolved using Sleuth and DESeq2 in R and signaling pathway analysis was performed using Ingenuity Pathway Analysis (IPA). Results reveal differential inactivation of the GPVI pathway and key cell survival and viability genes only in renal AML cells treated with imatinib conentrations.We further determined that this TKI differentially induced ER calcium efflux that disrupted mitochondrial permeability leading to increased cytosolic cytochrome C, caspase 3 activation and apoptosis. Overall design: Comparing total RNA profiles of renal angiomyolipoma cells treated with Rapamycin vs. Imatinib