2.1. Chemicals
SK-1, SK-2, SK-3, D-SK-4, L-SK-4 and SK-5 were previously synthesized, purified and characterized [18]. GSH, resazurin sodium salt and Myriocin were purchased from Sigma-Aldrich (St. Louis, MO, USA). All media and cell culture material were obtained from LabTech International Ltd (East Sussex, UK). Bovine Serum Albumin (BSA) was obtained from Biosera (Boussens, France). Protease and phosphatase inhibitor cocktails were obtained from Roche (Base, Switzerland). Polyvinylidene difluoride (PVDF) membranes (0.45 and 0.2 µm) were purchased from Millipore (Bedford, MA, USA). All solvents were of UHPLC optima grade or better.
2.2. Cell lines
A375 and A431 cells were purchased from Sigma-Aldrich (St. Louis, MO, USA). In addition, VMM1, Hs294T and B16F10 cells were obtained from LGC Standards (Middlesex, UK). All cell lines were maintained in a humidified atmosphere at 37 °C, 5% CO2 and according to the provider’s recommended culture conditions. All media and reagents were purchased from Labtech (East Sussex, UK). All plasticware were obtained from Corning (Corning, NY, USA).
2.3. Determination of cell viability
Briefly, A375 cells were seeded in 100 µL/well into 96-well plates and incubated overnight. On the following day, cells were exposed to either GSH (1.5-3.0 mM) or Myriocin (0-50 µM) with or without L-SK-4 (100 µM) over different incubation periods while control cells were incubated with complete medium only. The Alamar-blue assay was utilized as previously described [18].
2.4. Determination of ROS
Cells were seeded in 60 mm dishes and then exposed to L-SK-4 (100 µM) with or without pre-treatment with either GSH (1.5 mM) or Myriocin (50 nM). Then, they were harvested and washed twice with PBS after which, a single cell suspension of 106 cells/mL was prepared. Dihydrorhodamine 123 (DHR 123; 10 µM) was added in the suspension and incubated for 5 mins at 37 oC followed by addition of DAPI (1 µM), in each sample, and further incubation for 5 mins. Data acquisition and analysis of 10,000 events, for each sample, was performed using a FACS Canto II flow cytometer (BD Biosciences, San Jose, CA, USA). DAPI-positive cells were excluded from further analyses.
2.5. Determination of apoptosis
The CellEvent Caspase 3/7 Green flow cytometry assay kit was utilized for the detection of apoptosis according to the manufacturer’s instructions. Briefly, cells were seeded and allowed to adhere overnight in 60 mm dishes and then exposed to L-SK-4 (100 µM) with or without pre-treatment with either GSH (1.5 mM) or Myriocin (50 nM). Next, cells were harvested and washed twice with PBS after which, a single cell suspension of 106 cells/mL was prepared. Then, 0.5 µL of CellEvent Caspase 3/7 Green detection reagent was added into 0.5 mL of each cell suspension and samples were incubated at 37 oC for 30 mins followed by addition of DAPI (1 µM), in each sample, and further incubation for 5 mins. Data acquisition and analysis of 20,000 events, for each sample, was performed using a FACS Canto II flow cytometer (BD Biosciences, San Jose, CA, USA).
2.6. Determination of mitochondria membrane depolarization
The JC-1 staining solution was used according to the manufacturer’s instructions. Following treatment with L-SK-4 (100 µM) with or without pre-treatment with myriocin (50 nM), cells were harvested and washed twice in PBS. Then, 0.3 µL of JC-1 (0.1 mg/mL) was added into 0.3 mL of each cell suspension, in PBS, and samples were incubated at 37 oC for 30 mins. All cell suspensions were centrifuged at 1,000 rpm for 5 mins and pellets were re-suspended in fresh PBS. Data acquisition and analysis of 10,000 events, for each sample, was performed using a FACS Canto II flow cytometer (BD Biosciences, San Jose, CA, USA).
2.7. Preparation of cell lysates and protein determination
A375 cells were plated in 100 mm dishes and cultured overnight at 37 oC. Next day, cells were treated with L-SK-4 (100 µM) with or without pre-treatment with either GSH (1.5 mM) or myriocin (50 nM) for 24, 48 and 72 hr. Cell lysates were prepared and obtained as previously described [18]. Protein content was determined by utilizing the BCA protein assay kit (Thermo Scientific, Waltham, MA, USA), according to the manufacturer’s protocols. Protein extracts were stored at -20 oC until usage.
2.8. Western immunoblotting
Standard conditions were used as previously described [18]. All antibodies (e.g., anti-Caspases-8 and -9, anti-Apaf-1, anti-BID, anti-FADD, anti-FAS, anti-BAX, anti-BAK and anti-Tubulin) were purchased from Cell Signaling Technology (Danvers, MA, USA) and utilized according to the manufacturer’s protocol.
2.9. Determination of lipid peroxidation content
A375 cells were plated in 100 mm dishes, cultured overnight and next day were treated with L-SK-4 (100 µM). After trypsinization, pellets were collected, re-suspended and sonicated before the TBARS Assay kit (Cambridge Bioscience Ltd, Cambridge, UK) was utilized for the determination of malondialdehyde (MDA) content according to the manufacture’s protocol.
2.10. Determination of protein carbonyl content
A375 cells were plated in 100 mm dishes, cultured overnight and next day were treated with L-SK-4 (100 µM). After trypsinization, pellets were collected, resuspended and sonicated before the Protein Carbonyl Colorimetric Assay Kit (Cambridge Bioscience Ltd, Cambridge, UK) was utilized for the determination of protein carbonyl content according to the manufacture’s protocol.
2.11. Determination of oxidative DNA damage content
A375 cells were plated in 100 mm dishes, cultured overnight and next day were treated with L-SK-4 (100 µM). After trypsinization, pellets were collected and the dsDNA content was extracted using the PureLinKTM Genomic DNA Mini Kit (Invitrogen, Carlsbad, CA, USA) and then converted to ssDNA according to the manufacture’s protocol. The DNA/RNA Oxidative Damage (High Sensitivity) ELISA Kit (Cambridge Bioscience Ltd, Cambridge, UK) was utilized for the determination of 8-oxo-2-deoxy guanosine (8-OHdG) content according to the manufacture’s protocol.
2.12. Lipidomic extraction protocol
A375 cells were plated in 100 mm dishes and cultured overnight at 37 oC. Next day, cells were treated with L-SK-4 (100 µM) and then trypsinised and collected by centrifugation at 2,000 rpm for 3 mins at 4 oC. Approximately 3 x 106 cells were washed with ice-cold PBS three times prior to extraction. Then, the cell pellet was re suspended in 300 µL of the extraction buffer (dichloromethane/methanol (3:1 v/v) chilled to 4 oC) and cell lysis was induced by snap freezing the samples in liquid nitrogen for 1 min and thaw over ice. This was repeated 5 times to ensure complete cell lysis. Then, cell suspensions were sonicated for 15 mins and ultra-centrifuged at 15,000 rpm for 15 mins. The entire supernatant was transferred to 1.5 mL Eppendorf and allowed to evaporate, at RT, overnight under a fume hood. The dried down extracts were reconstituted in 300 µL of isopropyl alcohol/ACN/water (2:1:1), sonicated for 15 mins and ultra-centrifuged at 15,000 rpm for an additional 15 mins before transferring 100 µL to 1.5 mL autosampler vial, caped and then subjected to lipidomic characterization.
2.13. Lipidomic sample analysis
LC parameters: Chemical analysis was performed on a Thermo Scientific Orbritap classic mass spectrometer hyphenated to a Dionex 3000 UHPLC with the autosampler tray set to 4 oC. The separation was performed on a Waters C18 CSH analytical column, 2 x 100 mm with a 1.7 µm particle size. The column was maintained at 55 oC with a flow rate of 400 µL/min. A binary buffer system was used for the chromatographic separation. Buffer A was 60/40 (v/v ACN/MillQ water) and Buffer B (90/10 v/v isopropyl alcohol and ACN) with 10 mM ammonium formate and 0.1% formic acid.
LC profile: Starting condition: 00.00 min 45% (B) → 11.00 min 65% (B) → 20.00 min 99% (B) → 24.00 min 99% (B) → 24.25 min 45% (B) → 28.50 min 45% (B).
Mass spectrometer: The HESI source condition was as follows: Sheath gas flow: 50, Aux Gas flow: 13, Sweep gas flow: 3. Spray voltage was set 3.5 kV, Capillary temperature was set to 275. S-lens RF level was set to 50 and the temperature of the HESI was set to 425 oC.
Mass spectral acquisition parameter: Scan range was set from 300 to 2,000 m/z at mass resolution of 140K with a scan rate of 1.6 scans/sec with an automatic gain control of 1 x 106 with a maximum injection time of 100 ms. MS1 profiling in positive polarity mode.
Peak table generations: Compound discoverer V2, the alignment window was set to 0.25 mins with mass tolerance of 5 ppm with (M-H)+ adducts only. Quality control and extraction blanks were imbedded into the analysis for stability assessment and background subtractions.
2.14. Statistical analysis
Data were expressed as mean values ± standard deviation (SD) and comparisons were made between control and treated groups. Statistical analyses were performed by one-way ANOVA with Tukey’s test for multiple comparisons, by using the SPSS v.22 software, and statistical significance was set at p<0.05, p<0.01 and p<0.001. For the lipidomic analyses, all multivariate data analyses were performed using the metaboanalyst v3 web-based version (https://academic.oup.com/bioinformatics/article/34/24/4313/5046255).