GSE193398
Comparative RNA sequencing identifies superior cytocidal mechanisms of imatinib over rapamycin in Pulmonary Lymphangioleiomyomatosis (LAM) Tumor Cells
We report results of RNA sequencing analysis of serum starved pulmonary LAM tumor cells comparatively treated for 24hrs at 37C and 5% CO2 with rapamycin (0.05uM and 1uM) and tyrosine kinase inhibitor (TKI) imatinib (1uM, 5uM, and 10uM). Experiments were done in duplicates 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 20 milllion paired 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. Differential expression was resolved using Sleuth in R and signaling pathway analysis was performed using Ingenuity Pathway Analysis (IPA). Results reveal differential inactivation of the Cell Cycle: G2/M DNA Damage Checkpoint Regulation SIgnaling Pathway only in pulmonary LAM tumor cells treated with 10uM imatinib concentration.We further determined that increasing imatinib conentrations from 1uM to 10uM induced endoplasmic reticulum inositol triphosphate receptor (IP3R) subtype switching from type I to type III typically associated with differential ER calcium efflux and apoptosis. Overall design: Comparing total RNA profiles of pulmonary LAM tumor cells treated with Rapamycin vs. Imatinib