Expression of genes in HepG2 cells with Knock-out in cholesterol synthesis

HepG2 cell line CRISPR-Cas9 generated Knock-out in 4 cholesterol synthesis gene: CYP51, DHCR24, SC5D and HSD17B7 Excess of cholesterol associates with a variety of diseases so its synthesis must be under tight homeostatic control. The early part of cholesterol synthesis with rate-limiting HMGCR and SQLE steps is proceeded by the sterol part where numerous non-polar sterols with poorly defined biological functions are produced. To illuminate their role we developed knockouts (KO) for the consecutive enzymes that metabolize sterols towards cholesterol CYP51A1, DHCR24, SC5D resulted in the accumulation of specific set of sterols in each KO cell. Despite that, we targeted three steps of the cholesterol synthesis housekeeping pathway, the overlap of de-regulated genes was only 9%, suggesting that each set of sterols modulated the hepatic cell transcriptome uniquely. Lanosterol and 24,25-dihydrolanosterol, but not other non-polar sterols, provoked higher cell proliferation, cell cycle changes, and upregulation of metabolic pathways and transcription factors (TFs) associated with cancer progression and immune response like NFKB, SMAD, ESR1 and highly elevated LEF1 a protein from WNT signalling. In contrast, lathosterol and desmosterol caused slower proliferation and apoptosis promotion, through TFs like HNF1A and E2F. We were able to show how sterols from early part of synthesis can promote cell proliferation as sterols from end of synthesis suppress proliferation. These findings challenge the current dogma that sterols produced during cholesterol synthesis have similar biological functions Control HepG2 (named Native) and 4 lines each with Knock-out in one of the cholesterol synthesis genes: CYP51 KO, DHCR24 KO, SC5D KO and HSD17B7 KO were used to obtain tanscriptome data using Clariom S Array, human (902917, Applied Biosystems, Waltham, MA, USA). Each genotype had 3 biological replicates. Cell were seeded on 6-well plate in Dulbecco’s Modified Eagle’s Media (DMEM) high glucose (D6429, Sigma Aldrich, St. Louis, MO, USA), supplemented with 10% FBS (F0804, Sigma Aldrich, St. Louis, MO, USA) and 1% penicillin/streptomycin (P0781, Sigma Aldrich, St. Louis, MO, USA). Cells were cultured in constant 37 °C and 5% CO2. After 24h after seeding cell medium was changed with DMEM high glucose, supplemented with 10% LDP (Lipid Depleted Serum Biosera inc., France), 1% penicillin/streptomycin and 30 µg/ml of cholesterol (Sigma Aldrich). 48h after medium change, cell were washed 2 times with PBS and TRI reagent (T9424, Sigma Aldrich, St. Louis, MO, USA) was used for RNA isolation. Concentration was measured using Nanodrop and RNA quality using Agilent Bioanalyser. Transcriptome analysis was performed using Clariom S Array in triplicates from each cell genotype according to manufacturers protocol.