Transcriptomic profiling of LLC LeptoM vector control, Nr1h2/3 DKO and RXRa/b/g TKO upon stimulation with 1µM 9 cis-retinoic acid (RA) in vitro

To understand transcriptional regulation of nuclear receptors, LXRs and RXRs, in leptomeningeal metastatic cancer cells, we use CRISPR-Cas9 to knockout Nr1h2/3 genes (encoding LXRß/a) or RXRa/b/g genes (encoding RXRa/ß/?) in LLC LeptoM cell lines, with small guide RNA targeting lacZ as vector control. We then subjected these cell lines for bulk RNA sequencing with or without stimulation of 1µM 9 cis-RA. Pathway analysis of the differentially expressed genes between LLC LeptoM vector control with RA stimulation to DMSO treatment revealed upregulation of developmental related pathways and lipid metabolism pathways. Meanwhile, loss of function in LXR or RXR both resulted in dysregulation of multiple lipid metabolism pathways, in which RXR made a broader impact. Overall design: LLC LeptoM vector control, Nr1h2/3 DKO and RXRa/b/g TKO were seeded into 6 well plates and added either DMSO or 1µM 9 cis-RA one day after seeding. After treatment for 48hrs, cells were harvested with RNA lysis buffer and further processing for sequencing. This experiment has two to three biological replicates different rounds of collection.