3-Methyladenine (3-MA) was purchased from Sigma (Sigma-Aldrich, USA) and prepared as a stock solution of 100 mM in phosphate buffered saline (PBS). Paclitaxel, monodansyl cadaverine (MDC), and bafilomycin A1 were purchased from Sigma. U0126 was purchased from LC laboratories (LC Labs, USA).

GFP-LC3 plasmid was obtained from Addgene (Addgene plasmid 24920). HT TiterTACSTM Assay Kit was purchased from TREVIGEN (TREVIGEN, USA), Beclin 1 siRNA was purchased from Invitrogen (Invitrogen Life Technologies, NY, USA). Antibodies used in this study included the following: Anti-cleaved Caspase-3, anti-MEK1/2, anti-phospho-MEK1/2, anti-phospho-ERK1/2, anti-p62 and anti-Beclin 1 (Cell Signaling Technology, USA); anti- LC3 polyclonal (Thermo Fisher Scientific, USA); anti-FLCN antibody (Obtained from the Van Andel Research Institute). Cell culture Two pairs of cell lines were used: FLCN Etoposide nmr siRNA-silenced ACHN-5968 cell line and scrambled ACHN line (ACHN-sc); FLCN-null UOK257 cell line and UOK257-2 line restored with ectopic expression of FLCN. ACHN was purchased from ATCC, and ACHN-5968 was generated in our lab. UOK257 cell line was obtained from NCI, and UOK257-2 Dactolisib chemical structure was prepared in our lab. All of these cell lines were cultured in DMEM medium, supplemented with 10% fetal bovine serum (FBS) and maintained at 37°C with 5% CO2. Cell viability assay The viability of cells was measured by MTT

assay. Approximately 2 × 103 cells were cultured in 96-well plates and treated with various reagents. MTT (5 mg/ml) was added to each well and cells were cultured at 37°C for 4 hours. Supernatant was

removed and 200 μl DMSO per well was added to dissolve the formazan. Absorbance was measured at 570 nm Etomidate using a microplate reader (BioTek). Western blot Cells were harvested and lysed on ice for 45 min in RIPA lysis buffer (1 M Tris, PH7.4, 50 mM; NaCl 150 mM; 1%NP-40; EDTA 1 mM, plus standard protease inhibitor). The concentration of protein was measured by Nanodrop (Thermo). Equal amounts of total protein extracts were loaded and separated in 10% -15% SDS-PAGE gel and transferred to PVDF membranes. The membranes were blocked in Tris-buffered saline-Tween-20 (TBST) with 5% milk for 1 hour and incubated overnight at 4°C with different primary antibodies: mouse monoclonal anti-FLCN at a dilution of 1:1000, rabbit polyclonal anti-LC3-I/II (1:2000), rabbit polyclonal anti-p62 (1:2000), rabbit monoclonal anti-cleaved caspase-3 antibody (1:1500); mouse polyclonal anti-MEK (1:2000), rabbit polyclonal anti-phospho-MEK (1:2000); rabbit polyclonal anti-phospho-ERK (1:2000) or mouse monoclonal anti-Beclin 1(1:2000). The membranes were washed in TBST and incubated with secondary antibody at room temperature for two hours. Proteins were detected with ChemiDoc detection system (Bio-Rad). DAPI stain and TUNEL assay Cell apoptosis was detected using DAPI stain and TUNEL assay.