Bioinformatic analysis
The survival analysis of TCGA datasets and GEO datasets in ovarian cancer patients were performed on website (http://kmplot.com/analysis/index). GEO datasets (GSE15709) were used, data were downloaded from website (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE15709), and analyzed by R/R studio. DEGs (differential expressing genes) were extracted by limma R package, with the filter standard of log|FC| ≥1,p value<0.05, GO and KEGG pathway enrichments were performed by clusterProfiler R package[15]. The visualization of pathway was performed by Pathview R/Bioconductor package[16]. We calculated rich factor of KEGG enrichment comprehensively with gene numbers and weights using S4Vectors R package.
Cell lines and culture conditions
The human epithelial ovarian cancer cell lines A2780, SKOV3 and HEY were purchased from the Cell Bank of the Chinese Academy of Sciences in Shanghai, China. The HEY cells were cultured in DMEM with 10% fetal bovine serum, A2780 and SKOV3 cells were cultured in RPMI-1640 medium along with 10% fetal bovine serum. All kinds of the culture medium were added 100U/ml penicillin and 100ug/ml streptomycin. Cells were maintained at 37℃ with 5% CO2 and 95% air.
Induction of cisplatin resistance
The parental A2780 cells were exposed to repeated and gradual elevated concentration of cisplatin (MCE, NJ, USA) over a year period, with the concentration of cisplatin gradually increasing from 2μM to 50μM.
Cell viability and colony formation assays
MTT assay was used to detect cell proliferative ability. To examine the proliferative ability, cells were inoculated into 96-well plates, each well contained 800-1000 cells, incubated overnight to adhere. At fixed time from day 1 to day 5, 10μl MTT solution (5mg/ml, sigma, CA, USA) was added into every well, then put the plate back to incubate at 37℃ for 4H. The supernatant was carefully suctioned and 100μl DMSO (MP Biomedicals, OH, USA) was added into every well. After formazan fully dissolved, put the plate in the microplate reader (Tecan Group Ltd, Männedorf, Switzerland), reading the absorbance at 490nm.
For colony formation assays, 800 single cells were seeded in 6-well plate and mix with 2ml cultural medium. After incubated at 37℃ for 12 days, cells were fixed with methanol and stained with 0.1% crystal violet (Beyotime, Beijing, China).
Drug resistance assay
MTT assay was used to measure the surviving fractions and IC50 of cells. Cells were seeded into 96-well plate with cell concentration of 3000 cells per well, after exposure to different concentration of cisplatin and incubating for 24-72H. Finally, results were measured by microplate reader as mentioned above.
Cell cycle assay
Cells were harvested and fixed with ethanol when density of cells reached 80%, then stained with propodeum iodide according to protocol (BD, NJ, USA). The treated cells were harvested by flow cytometer (FACSCalibur, BD, USA). The results analyzed through Modifit LT software.
Cell apoptosis assay
Cells transfected with lentivirus or exposure to different concentration of cisplatin were harvested with tyrisin without EDTA, washed with PBS for 3 times, resuspended with Annexin binding buffer reaching a concentration of 1 106 per 100μl. Then cells were dyed with 5μl Annexin V-APC and 10μl 7-AAD (MultiSciences, Hangzhou, China), incubated with room temperature for 5 minutes. Finally, cells were collected with flow cytometer (FACSCalibur, BD, USA), and analyzed with Flowjo V10 software.
Lentivirus production and stable transfections
The plasmid containing shACLY and corresponding negative control (NC) were purchased from Genechem (Shanghai, China). The HEK279T cells were used to produce lentivirus. The shACLY plasmid were transfected in HEK293T cells together with pMD2.G and psPAX2. The obtained lentivirus was used to infect ovarian cancer cells for 12H. Cells were cultured with medium containing 2 μg/mL puromycin (Solabio, Beijing, China) to get the stable transfected cells.
Transient transfection
The plasmid containing AKT and corresponding NC were purchased from Genechem (Shanghai, China). Lipo3000 (Invitrogen, USA) was used to transfect plasmid into cells. Cells then harvested after 24–48 h for the following assays
Western blotting assays
Adherent cells were washed by PBS for 3 times, lysed with RIPA Lysis Buffer (Beyotin, Beijing, China) with 1% PMSF and 1% NaF, placed on the ice for 30 minutes. The contents were collected and centrifuged to get the supernatant as protein. The concentration of protein was measured by BCA reagents assays (Beyotime, Beijing, China). Adequate volume of 5×loading buffer was added into the protein and reaching the final concentration of 1×, and followed by metal bath. Samples were loaded into SDS-PAGE (10% separation gel or 12% separation gel) with 30μg per well, electrophorese to separate the protein in the page, then transferred to 0.22-μm polyvinylidene fluoride membranes (Merck Millipore, USA). Membranes were blocked in 5% skimmed milk for 1 hour, then incubated in primary antibodies overnight in 4℃, washed with 1×TBST, incubated in HRP-linked secondary antibodies respectively at room temperature for 1.5H or less. The chemiluminescent substrate (Thermo Fisher Scientific Inc, MA, USA) were used to detect bands on membranes under Image Quant LAS 4000 (GE Healthcare Life Science). GAPDH was detected as the endogenous control.
Tumor xenograft experiment
The A2780 and A2780/CDDP cells stably expressing shACLY and corresponding NC cell lines were used to construct in this procedure. Cells were harvested, counted to 1×107 and resuspended in 200μl PBS were injected subcutaneous on either side of axilla of the 4-6week old nude female mice. Tumor sizes were measured every other day from day 10 after injection. The mice compromise A2780/CDDP cells were received cisplatin injection intraperitoneally with a concentration of 4 mg/kg body weight (B.W.) on day 7, 14 and 28 (total three injections). Mice were sacrificed 35 days after A2780 cells injection and 4 weeks after cisplatin injection in A2780/CDDP cells group. The volumes of tumors were calculated as V=[(length × width2)/2].
Antibodies and chemical inhibitors
The antibodies of ACLY, p16 ARC and PFKM were purchased from Abcam (Cambridge, UK). The antibodies of cleaved PARP, TP53, pan-AKT, phosphorylated-AKT (Ser473), phosphorylated-AMPK-α and GAPDH were purchased from Cell Signaling Technology (MA, USA). SB-204990 was purchased from MCE (NJ, USA).
Measurement of intracellular ROS levels
The intracellular ROS levels were measured using a Reactive Oxygen Species Assay Kit (Beyotime Shanghai, China). 3000 cells were seeded in each well of 96-well plates as and exposed to 20μM of cisplatin for 24H. Following the treatment, the cells were incubated with DCFH-DA for 20min at 37°C and then measured at 488 nm excitation and 525 nm emission by a fluorescence microplate.
Statistical analysis
All experiments were repeated at least 3 times. GraphPad Prism 8.0.1 (GraphPad Software, USA) was mainly used in data analyzing. Student’s t test and one-way ANOVA analysis were applied to determine the statistical differences among different groups. Persistent variable was presented mainly by means±SD. IC50 of cells were presented as best fit value with 95%CI. P <0.05 was regarded as statistically significant.