Cells and cell culture
Bladder cancer cell lines T24, HT1376, RT4, and human embryonic kidney 293 (HEK293) cells were purchased from the American Type Culture Collection(ATCC). The cells were cultured in RPMI-1640 medium (Gibco; Thermo Fisher Scientific, Inc.) supplemented with 10% FBS (Gibco; Thermo Fisher Scientific, Inc.), 1% MEM Non-Essential Amino Acids (Gibco; Thermo Fisher Scientific, Inc.), 1% MEM sodium pyruvate solution 100 mM (Gibco; Thermo Fisher Scientific, Inc.) and 90 µg/ml kanamycin in a 37°C incubator containing 5% CO2.
Passaging was achieved using 5 ml 0.05% Trypsin-EDTA (Gibco; Thermo Fisher Scientific, Inc.) when cells were fused to 80%. AR-A014418 and TDZD-8(GSK-3 inhibitor) were purchased from Abcam.
Cell viability assay
The cells were seeded in 96-well plates at 1–2×103–4 cells/well with 100 µl medium for 24 hours and then treated with AR-A014418 at the indicated concentrations (0, 0.5, 1, 5, 10, and 25 µM) for 24, 48, and 72 hours. Following incubation, 10 µl CellTiter 96 Aqueous One Solution Regent(Promega Corporation) was added into each well and incubated for 2 hours. The absorbance was measured at 490 nm by the iMark™ 96-well microplate reader (Bio-Rad Laboratories, Inc.). Chloroquine(phosphate) (14194) was purchased from Cayman chemical company.
Protein Extraction and Western blot analysis
Subconfluent cell cultures were washed with cold PBS and lysed in lysis buffer (20 mM Tris-HCl (pH 7.5), 150 mM NaCl, 1 mM Na2EDTA, 1 mM EGTA, 1% Triton, 2.5 mM sodium pyrophosphate, 1 mM beta-glycerophosphate, 1 mM Na3VO4, 1 µg/ml).
Following clarification of the lysates by centrifugation at 15,000 × g for 30 min at 4°C, protein concentration was detected by the Bradford method, and 20–30 µg of each protein was electrophoretically separated on a 4–15% or 10 or 7.5% SDS-polyacrylamide gel and transblotted to a PVDF membrane. Immunoblots were blocked with 10% skimmed milk in TBS followed by incubation with primary antibodies. Horseradish peroxidase-labeled ECL™ Anti-mouse IgG (1:5,000) and ECL™ Anti-rabbit IgG (1:10,000) from GE Healthcare were used as secondary antibodies and detected using Clarity Max Western ECL Substrate from Bio-Rad Laboratories, Inc. according to the manufacturer's instructions. The expression of β-actin(Cell Signaling Technology, Inc., 12262) was used as a loading control. The images were analyzed using Ez-Capture MG (Atto Corporation). The following primary antibodies were purchased from Cell Signaling Technology, Inc.: SQSTM1/p62(8025), Beclin-1(3738), p-Beclin-1(S15)(84966), p-Beclin-1(S93)(14717), LC3(3868), GSK3β(12456), TFEB(4240), α-Tubulin(9099), Histone3(12648), p-ULK1(14202), ULK1(8054), p-AMPKα(2535), AMPKα(5831).
The dilution ratios of the primary antibodies were 1:200-1:2,000.
Nuclear/cytosolic fractionation was carried out by the Minute™ Cytoplasmic and Nuclear Extraction Kit for Cells(Invent Biotechnologies, Inc., SC-003) according to the manufacturer's instructions. α-Tubulin and Histone3 were used as a control for cytosolic and nuclear lysates respectively.
Estimation of autophagic flux
pMRX-IP-GFP-LC3-RFP-LC3ΔG(plasmid # 84572) was purchased from Addgene, Inc. The plasmid was transformed into NEB stable Competent E.coli (New England Biolabs, Inc., C3040H) and plasmid DNA was extracted and purified by PureLink™ HiPure Plasmid Midiprep Kit(Invitrogen; Thermo Fisher Scientific, Inc.).
The cells(70–90% confluent) were grown in 24-well plates and transfected with the plasmid according to the Lipofectamine™ 3000 Reagent protocols. After 24 hours incubation, the cells were treated with 10µM AR-A014418 for 12, 24, and 48 hours, and images were captured by fluorescence microscope(Olympus, IX71) at 40x magnification. The absorption filters used were BA510IF for green fluorescence and BA575IF for red fluorescence. The fluorescence intensity was quantified using the ImageJ imaging software program.
Nuclear translocation of TFEB-EGFP
pEGFP-N1-TFEB (plasmid#38119) was purchased from Addgene, Inc. The plasmid was transformed into competent high DH5α(TOYOBO CO., LTD., DNA-903) and plasmid DNA was extracted and purified by PureLink™ HiPure Plasmid Midiprep Kit(Invitrogen; Thermo Fisher Scientific, Inc.).
The cells(70–90% confluent) were grown in 24-well plates and transfected with the plasmid according to the Lipofectamine™ 3000 Reagent protocols. After 24 hours incubation, the cells were treated with 10 µM AR-A014418 for 24 hours and nuclear translocation of TFEB-EGFP was examined and analyzed by fluorescent microscopy(Olympus, IX71) at 40x magnification. The absorption filters used were BA510IF for green fluorescence. The nuclei were stained with Hoechst 33342(Bio-Rad Laboratories, Inc., 1351304) 5 µg/ml for 10 min at room temperature.
siRNA transfection
For GSK-3β silencing, the cells were transfected with specific human siRNAs against GSK-3β by using Lipofectamine RNAiMAX(Invitrogen, Thermo Fisher Scientific Inc.) according to the manufacturer’s recommendations. siRNA targeting human GSK-3β(s6239, s6241) and control siRNA with a scrambled sequence(AM4611) were purchased from Ambion, Thermo Fisher Scientific, Inc. Targeting sequence of siRNA are as follows: GSK-3β(s6239); CUCAAGAACUGUCAAGUAAtt, GSK-3β(s6241); GCUAGAUCACUGUAACAUAtt. The knockdown efficiency was then measured by immunoblotting.
Statistical analysis
Continuous variables are presented as the mean ± SD. All continuous variables in this study met the criteria for normal distribution and were assumed to be parametric. Data were analyzed using one-way ANOVA with Dunnett's test for multiple comparisons. Statistical analysis was performed using GraphPad Prism 8 software (GraphPad Software, Inc.). P < 0.05 was considered to indicate a statistically significant difference.