Main reagents, Antibodies, and KAN0438757
Protease-phosphatase inhibitor cocktail, trypan blue, Tris HCl, trypsin-EDTA, dimethyl sulfoxide (DMSO), TEMED, Sodium azide (NaN3), luminol, Skim milk powder, P-coumaric acid, bovine serum albumin (BSA) and others was obtained from Sigma Aldrich company. Dulbecco’s modified Eagle’s medium (DMEM) fetal bovine serum (FBS), penicillin/streptomycin, and phosphate buffered saline (PBS) were purchased from Gibco. WST-1 assay was obtained were obtained from Boster (USA). GAPDH, p62, Beclin 1, LC3, PARP antibodies used in Western blot studies were obtained from SantaCruz Biotechnology (USA), and Anti-mouse antibody was obtained from Invitrogen (USA).
PFKFB3 inhibitor KAN0438757 (Cat No: S0400) was purchased from Selleck Chemicals GmbH (Houston, TX 77014 USA). It was dissolved in sterile dimethyl sulfoxide (DMSO, sterile-filtered, suitable for cell culture) at a final concentration of 1 mM, then stored in aliquots at −80°C and working concentrations were diluted in culture medium.
Cell Lines and Culture Conditions
All cell lines used (A549, H1299, and COS7) cell lines were provided by ATCC (American Type Culture Collection, Manassas, USA). A549 and COS7 were maintained in DMEM (Dulbecco’s modified Eagle’s medium containing with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin (Gibco, Grand Island, NY, USA). H1299 cells were cultured in RPMI (Roswell Park Memorial Institute) 1640 medium added with 10% FBS and 1% penicillin-streptomycin. Cell lines used in this study were grown by culturing at 37 °C, 95% humidity and 5-6% CO2.
Cell Viability
The viability of A549, H1299, and COS7 cells was assessed with the WST-1 assay kit (Boster, USA). Briefly the cells were treated with KAN0438757 at concentrations of 1, 5, 10, 25, 50, and 100 µM) and time point (24, 48, 72h). Then, 10μl WST-1 solution was added into the wells. The plates were kept out of light and incubated in a 37°C CO2 (5%) incubator for 3h. Afterthat, it was measured spectrophotometrically at 420-480 nm using an ELISA microplate reader (Spectra Max 384 Plus).
Real-Time Cell Analysis (RCTA)
A549 and H1299 cells (1.5×104 cells/well ) and A549 cells (1×104 cells/well) were plated into the E-Plate16 and then incubated in xCELLigence RTCA instrument (ACEA Bioscience, CA, USA) at 37°C and 5% CO2. E-16 plates have microelectrodes to measure the cellular impedance which was recorded every 15 min for 96 h by xCELLigence RTCA. After attaching them to the plate, the cells were given different doses of KAN0438757 and then incubated for 48 hours. Recorded data were analyzed by RTCA Software (v1.2, ACEA Biosciences Inc.).
Clonogenic Survival Assay
Clonogenic survival assay was performed as described earlier [24]. Briefly, in this experiment, the cells were seeded on six-well plates at 800 cells/well, and cultured overnight, after which they were incubated with indicated doses of KAN0438757 for 48 h. After 12 days of treatments, cells were fixed with methanol-acetic acid for 12 minutes and stained with 0.5% crystal violet for 15 minutes at room temperature and colonies were counted (>50).
Single Cell Gel Electrophoresis (Comet Assay)
A549 cells were seeded in 6-well plates (2 x105) and treated with incubated with indicated doses of KAN0438757 for 48 h. At the end of the incubation, the wells were washed with PBS and the cells were dissociated using trypsin. The cells were then centrifuged and re-suspended with PBS and mixed with 0.5% low melting point agarose (LMA). After taking 20 μl of this mixture, it was spread on a slide covered with normal melting point agarose (NMA) and the agarose was frozen at 4 °C by covering the coverslip for 45 minutes. Coverslips were removed and placed in cold lysis solution (2.5M NaCl, 100mM EDTA, 10mM Tris, 10% DMSO, 1% Triton X-100, (pH 10)) at 4 °C for 60 min. Slides were rinsed with PBS and placed in a buffer-filled gel electrophoresis. Electrophoresis was performed at 28V, 300 mA for 25 minutes and slides were neutralized with solution (pH 7.5) and rinsed with PBS. Slides were stained with Ethidium bromide (10 µg/mL) for 15 minutes and viewed under a fluorescent microscope. Opencomet program was used for analysis.
Wound-Healing Assay
Cells were seeded in 6-well cell culture dishes at 25x104 in each well. After the cells adhered to the surface, the cells were scraped to form a straight line with the help of a 20 µl pipette tip. Each well was washed twice with PBS so that the removed cells would not re-adhere to the surface. Wound areas were observed with an inverted microscope and photographed at 0, 24, and 48 hour time periods [17].
Acridine Orange And Ethidium Bromide double staining
Acridine orange and Ethidium bromide (EtBr/AO) staining was performed according to the protocol described previously [18]. A549 cells were treated with the indicated doses of KAN0438757 and then EtBr/AO(1:1) and added to the wells for 15 minutes at room temperature. Stained cells were observed with a fluorescence microscope (Olympus, Japan).
Mitochondrial membrane potential (ΔΨm) Assay
Monolayers cells in the logarithmic growth stage were inoculated into glass-bottom culture plates at 2×105 cells per well. Then, cells were treated with KAN0438757 for 48h. Slides were then washed and stained with the cationic dye JC-1 (5 mg/mL) for 15 min at 37 °C. The stained cells were analyzed by fluorescence microscope (Olympus, Japan). After staining, seven areas per well were randomly captured by the microscope. Each experiment was repeated at least three times.
Protein Isolation and Western Blot Analysis
Cells were collected with a plastic scraper by washing three times with cold PBS after 48 hours of treatment and transferred to numbered microcentrifuge tubes. After centrifugation at 6600 rpm for 10 minutes, it was dissolved in lysis (RIPA) buffer and then incubated on ice for 60 minutes. After the incubation period, it was centrifuged for 10 minutes at 14,000 rpm at 4°C. Protein content in the supernatants was measured by their absorbance at 595 nm in the spectrophotometer using BSA as a standard. (Biomethod-GBC (Bradford)). With the help of electrophoresis system (Bio-RadTrans-Blot cell, BioRad, USA), protein samples and marker were fractionated on SDS-PAGE (10-12%) gel. Then, the proteins separated in the gel were transferred to Polyvinylidenedifluoride (PVDF) membrane. Blockage was made with BSA to close the pores in the membrane. The membrane was incubated overnight with primary antibodies first and then with secondary antibodies. Subsequently, washing was done with TBS-T. The results were determined by chemiluminescence method so that the membranes were visualized by X-Ray device.
Statistical Analyses
Statistical analyses were performed using the GraphPad Prism software (USA). Data were obtained from three separate experiments. Statistical analysis was analyzed with Graph Pad Prism 8.0.2 program according to multiple comparison Post-Hoc Tests in “One-way ANOVA” method or independent two-sample Student’s ttest . P < 0.05 was accepted as significant in the analyzes.