Data acquisition
The study employed TCGA database data (https://portal.gdc.cancer.gov/), concentrating on EOC datasets to acquire RNA-seq, simple nucleotide variation (SNV) data, and clinical information from diverse brain sites.The transcriptome data included mRNAs from 427 tumor samples and 89 matched-normal samples.Clinical data were available for 565 patients, while SNV data were available for 407 patients, with 408 patients having accessible RNA-seq data and corresponding clinical information.Perl scripts (version 5.30; https://www.perl.org) were employed to extract clinicopathological details.
Liu (Liu X et al,2023) identified ten disulfidptosis-related genes relevant to this study. A total of 564 genes were obtained from the ferroptosis database (http://www.zhounan.org/ferrdb/current/).Spearman's correlation analysis (Cor > 0.3, P < 0.05) was conducted to explore the relationships between these genes, and the findings were visualized with a Sankey diagram.
The construction and validation of a risk model
This study employed the training set to construct a risk model centered on disulfidptosis-associated ferroptosis genes. The risk score was computed using the formula: (SLC1A5 * 0.2381) + (BRPF1 * 0.3792) + (RB1 * 0.2273) + (BCAT2 * 0.4241) + (ARF6 * 0.2824) + (GPT2 * 0.4271). The median risk score from the training set was used to stratify samples into low-risk and high-risk groups. The accuracy of the risk model was evaluated by generating ROC curves and calculating the C-index. Nomograms and calibration curves were generated with the 'survival,' 'replot,' and 'rms' packages to evaluate the model's predictive performance. Kaplan-Meier analysis and the log-rank test were used to compare survival outcomes across different risk categories.
Cell culture
The human ovarian cancer cell lines SKOV3 and A2780, as well as the human ovarian epithelial cell line IOSE-80, were sourced from the American Type Culture Collection (ATCC).A2780 cells were cultured in 1640 medium(Gibco, Grand Island, NY, USA), while SKOV3 and IOSE-80 cells were cultured in DMEM medium(Gibco, Grand Island, NY, USA), supplemented with 10% FBS (BI, Shanghai, China)and Penicillin/Streptomycin at 37°C in a humidified atmosphere with 5% CO2.
Antibodies, reagents, and siRNAs
Antibodies for BCAT2, GYS1, c-MYC, and CDK1 were obtained from Abcam (Cambridge, MA, USA), whereas those for E-cadherin, N-cadherin, Snail, Slug, CDC25C, and IgG were acquired from Cell Signaling Technology (Boston, MA, USA). Protein A/G was sourced from Thermo Fisher Scientific. The anti-β-actin antibody, serving as an internal control, was obtained from ZSGB-BIO (Beijing, China).Erastin was acquired from MCE (Sigma Aldrich, Shanghai, China).Two distinct BCAT2-specific siRNAs were designed by Huzhou Hippo Biotechnology Co., Ltd (Huzhou, Zhejiang, China).Specific siRNAs sequences for BCAT2 were showed in Supplement Table 1.
RNA extraction and qRT-PCR
Total RNA was extracted as per the manufacturer’s protocol, and 1 µg was reverse-transcribed into complementary DNA (cDNA). The primer sequences used were in Supplement Table 2. Real-time PCR was performed using the TAKARA kit protocol, starting with a pre-denaturation step at 95℃ for 30 seconds, followed by 40 cycles of 95℃ for 5 seconds and 60℃ for 34 seconds. Amplification and melting curves were generated, and data were analyzed using the 2−Δct method. Each sample was tested in triplicate.
Western blot
Protein quantification was performed using the BCA method, and the separated proteins were obtained via SDS-PAGE. The primary antibody (1:1000) was incubated overnight and the secondary antibody (1:20000) was incubated for two hours.Finally, the target bands were visualized by fluorescence scanning using the BIO-RAD gel imaging system.β-actin was used as the internal reference. Each experiment was conducted thrice.
CCK8 assay
5000 treated SKOV3 cells per well were seeded into a 96-well plate.100 µL of fresh medium with 10% CCK8 solution (Jiangsu KeyGEN BioTECH Corp., Ltd, Jiangsu, China) was added, followed by a 2-hour incubation at 37°C. Absorbance at 450 nm was then measured using a Multiskan Spectrum 1500 spectrophotometer (Thermo, USA).
Colony-formation assay
BCAT2-silenced cells were seeded in 6-well plates at a density of 1000 cells per well and incubated at 37°C for 14 days.The cells were fixed with methanol, stained with crystal violet, and colonies with over 50 cells were counted.
Assay for EdU (5-ethynyl-2-deoxyuridine)
Treated-SKOV3 cells were seeded at 3000 cells per well in 96-well plates and incubated overnight at 37°C.An EdU assay was performed following the manufacturer's guidelines (Jiangsu KeyGEN BioTECH Corp., Ltd).The cells were promptly examined using a fluorescence microscope, with each sample tested in duplicate.
Flow cytometry (FL)
Cell apoptosis was assessed after 48 hours by counting cells after digestion with EDTA-free trypsin.1×10^6 cells were labeled with FITC/PI dye and analyzed using a BD LSRFortessa flow cytometer (New Jersey, NJ, USA) in triplicate.For cell cycle analysis, after digestion and counting, cells were lysed using RNAase, fixed in 70% ethanol for 2 hours, and stained with PI dye. Data were processed and analyzed using FlowJo (FlowJo_v10.8.1).
Transwell migration and invasion
In the Transwell migration assay, 3 × 10^4 cells were seeded in the upper chamber of a Transwell insert within a 24-well plate, using 1% FBS medium in the upper chamber and 20% FBS medium in the lower chamber. After 24 hours, the chambers were fixed in 4% paraformaldehyde for 10 minutes, air-dried, and stained with crystal violet.For the Transwell invasion assay, 5 × 104 cells were seeded in the upper chamber, with the chambers coated with matrix gel. After 48 hours, the same steps as in the migration assay were followed.
ROS assay
The impact of reactive oxygen species (ROS) production was assessed using the ROS Assay Kit (Jiangsu KeyGEN BioTECH Corp., Ltd). After the treatment period, the cells were incubated with a 10 µM DCFH-DA probe for 1 hour at 37°C.The fluorescent signal intensity, indicating the ROS levels, was recorded using fluorescence microscopy.
JC-1
Mitochondrial membrane potential was evaluated with the JC-1 assay kit (Jiangsu KeyGEN BioTECH Corp., Ltd). SKOV3 cells underwent a 24-hour treatment with 2.5 µM Erastin.The cells were incubated with JC-1 reagent in PBS at 37°C for 15 minutes. The intensity of the mitochondrial membrane potential fluorescence signal was captured using fluorescence microscopy, with red fluorescence representing early apoptotic cells and green fluorescence indicating normal cells.
Co-immunoprecipitation(Co-IP) binding protein profiling
The supernatant from Erastin-treated SKOV3 cells was collected and divided into three groups: the Flag IP group, the IgG IP group, and the Input group.The supernatant from both the BCAT2 and IgG IP groups was incubated overnight at 4℃ in a chromatography cabinet with 5 µL of either rabbit anti-BCAT2 monoclonal antibody or anti-rabbit IgG antibody, followed by the addition of loading buffer. Protein mixtures were then subjected to identification by Shotgun LC-MS/MS mass spectrometry.
Statistical analysis
Data analysis was conducted using R software (v4.2.1) and GraphPad Prism 8.01 (La Jolla, CA, USA). Statistical inference for categorical data utilized the Chi-square test, while the t-test or Wilcoxon test was selected based on data normality and variance homogeneity. P-value < 0.05 was considered statistically significant.