Gene expression data acquisition
Bulk-sequencing data in count form and the survival information of 379 ovarian cancer patients were downloaded from The Cancer Genome Atlas (TCGA) database (https://portal.gdc.cancer.gov/), while the transcriptome data of 180 normal ovary samples were downloaded from the Genotype-Tissue Expression (GTEx) database (https://gtexportal.org/home/). Moreover, microarray data of 487 ovarian cancer samples and 22 normal ovary samples were downloaded from the Gene Expression Omnibus (GEO) (https://www.ncbi.nlm.nih.gov/geo/) database. Detailed information on the five GEO datasets (GSE18520, GSE54388, GSE9891, GSE63885 and GSE40595) is listed in Table S1[25-29].
Identification of differentially expressed genes (DEGs)
In the GEO cohort, the batch effect among different GEO datasets was removed by the “combat” function of the “sva” package in R software[30]. After batch removal, the data were used to identify the DEGs between ovarian cancer and normal ovarian tissues. In detail, significant DEGs were screened by the “limma” package with |log2foldchange| > 50 and adjusted P value < 0.01[31]. In the other cohort, DEGs were identified by the “DESeq2” package between 379 ovarian cancer (TCGA database) and 180 normal ovary tissues (GTEx database) with |log2foldchange| > 4 and adjusted P value < 0.01. Significant DEGs were identified by taking the intersection of these two cohorts. Subsequently, functional enrichment analyses were conducted by the “clusterProfiler” package[32].
Screening of the core hub genes
First, survival-related DEGs were screened by the random forest method using the “survivalsvm” and “randomForestSRC” packages. Next, a protein‒protein interaction (PPI) network was constructed based on these significant prognostic genes by the STRING database (https://cn.string-db.org/). The prognostic values of the core hub genes were further validated by the web-based Kaplan‒Meier plotter tool (https://kmplot.com/analysis/), and the protein expression levels of the core hub genes were determined through the Human Protein Atlas (HPA) database (https://www.proteinatlas.org/).
Clinical samples
Paraffin-embedded samples, including 90 EOC and 30 normal ovarian tissues, were obtained from the Second Xiangya Hospital between 2016 and 2018. Thirty fresh EOC and 15 normal ovarian tissues were obtained from the Second Xiangya Hospital between 2019 and 2020. None of these EOC patients underwent chemoradiotherapy, radiotherapy or targeted therapy before surgery. Normal ovarian tissues were collected from adenomyosis or hysteromyoma patients who underwent whole-uterus and double-attachment resection. The study was conducted in accordance with the Declaration of Helsinki and was approved by the Research Ethics Committee of the Second Xiangya Hospital of Central South University.
Immunohistochemistry (IHC)
IHC was performed using streptavidin-peroxidase method kit (ZSGB-BIO, China) according to the manufacturer’s protocol. Before dewaxing, the sections were placed in a 60 °C incubator for 20 min, deparaffinized in xylene and rehydrated in gradient concentrations of ethanol. Antigen retrieval was performed by heating the sections at 100 °C for 15 minutes in sodium citrate buffer (Wellbiology, China). To block endogenous peroxidase activity, 3% hydrogen peroxide was added to the sections for 15 min in the dark and incubated with 5% goat serum at room temperature for 20 min. Then, the corresponding antibodies were added to the sections and incubated overnight at 4 °C. The antibodies used were as follows: NCAPG (1:200, Proteintech) and Ki-67 (1:1000, Proteintech). After being washed with PBS, the sections were incubated with secondary antibodies for 30 min at 37 °C. Finally, the sections were stained with diaminobenzidine (DAB) and counterstained with hematoxylin. The IHC score was calculated by multiplying the intensity and the percentage scores.
Western blotting
Total proteins of tissues and cells were extracted using RIPA buffer (CST, USA) with proteinase inhibitor cocktail I (Merck, GER) for 20 min at 4 °C and then centrifuged at 15000 × g for 15 min. The supernatants were collected, and the protein concentration was measured using BCA Protein Assay Kit (Beyotime, China) and then diluted with SDS‒PAGE Loading Buffer 5x (Cwbio, China). A total of 15 μg of protein was separated by 8% or 10% SDS‒PAGE and then electroblotted onto a 0.45 μm PVDF membrane (Millipore, USA). After blocking with 5% fat-free milk or 5% bovine serum albumin for 1.5 h at room temperature, the membranes were incubated with primary antibodies at 4 °C overnight. Next, the membranes were incubated with corresponding secondary antibodies (Proteintech, China) at room temperature for 1 h. Finally, immunoreactive bands were visualized using enhanced chemiluminescence detection reagent (Thermo Fisher Scientific, USA) by Amersham Imager 600 (Cytiva, USA). The antibodies used were as follows: NCAPG (1:2000, Abcam), Vimentin (1:5000, Abcam), GAPDH (1:20000, Proteintech), BCL2 (1:5000, Proteintech), Caspase9 (1:1000, Proteintech), CDK4 (1:5000, Proteintech), CCND1 (1:5000, Proteintech), AKT (1:1000, CST), p-AKT (1:1000, CST), P65 (1:1000, CST), p-P65 (1:1000, CST), mTOR (1:1000, CST), and p-mTOR (1:1000, CST).
RNA extraction and qRT‒PCR
Total RNA was isolated from tissues and transfected cells by using RNAiso Plus reagent (Takara, Japan). cDNA was synthesized from 1 μg of total RNA using the Evo M-MLV RT Kit (AG Bio, China). qRT‒PCRwas carried out on the LightCycler®96 system (Roche, CH) and used the SYBR® Green Premix Pro Taq HS qPCR Kit (AG Bio, China). The expression of NCAPG was normalized to that of GAPDH. The polymerase chain reaction (PCR) thermal conditions were as follows: initial denaturation at 95 °C for 30 s, followed by 40 cycles of two-step PCR 95 °C for 5 s, 60 °C for 30 s and, finally, 95 °C for 15 s, 65 °C for 1 s, and 95 °C for 1 s for the dissociation curve. The 2-ΔCT method was used to analyze relative gene expression.
Cell culture
The human ovarian cancer cell lines OV90, SKOV3, A2780, and OVCAR3 were obtained from Zhong Qiao Xin Zhou Biotech (Shanghai, China). Cells were cultured in RPMI 1640 (Gibco, USA) medium supplemented with 10% FBS (BI, USA) and penicillin and streptomycin (Gibco, USA). All cell lines were incubated in an atmosphere of 5% CO2 at 37 °C.
Cell transfection and lentiviral infection
shRNAs and NC-shRNAs of NCAPG were synthesized by RiboBio (Guangzhou, China). shRNAs and NC-shRNAs were transfected into A2780 cells according to the instructions for the Lipofectamine 2000 reagent (Thermo Fisher Scientific, USA). Western blotting and qRT‒PCR assays were used to screen the best knockdown efficiency of the shRNA sequence for constructing lentivirus stable knockdown cell lines. Lentiviruses overexpressing NCAPG (LV-NCAPG) and its negative control (LV-NC), as well as lentiviral-based shRNA targeting NCAPG (LV-shNCAPG) and its negative control (LV-shNC), were purchased from Genechem (Shanghai, China). SKOV3 cells were infected with LV-NCAPG and LV-NC at multiplicity of infection (MOI) 160 and 80, respectively. A2780 cells were infected with LV-shNCAPG and LV-shNC at MOI of 40 and 80, respectively. After transfection for 96 h, SKOV3 and A2780 cells were selected for 1 week with puromycin at 3 μg/ml and 2.5 μg/ml, respectively, to establish stable cell lines.
Cell migration and invasion assays
Cell migration and invasion assays were performed with uncoated and Matrigel-coated (BD, USA) Transwell chambers (Corning, USA) with an 8 μM pore size. The stable cell lines (2x104/well) were suspended in 200 μl serum-free medium and seeded into the upper chambers, and 700 μl 10% FBS medium was added into the lower chambers. After 48 h of incubation, the cells on the lower side of the chambers were fixed with 4% paraformaldehyde and stained with 0.5% crystal violet (Beyotime, China). Migrated or invaded cells were photographed and counted under a light microscope at 20x magnification.
Cell proliferation, cell cycle and apoptosis analysis
Cells (2x103/well) were seeded into 96-well plates. At 0, 24, 48, 72 and 96 h, 10% CCK8 was added and incubated for 1 h, and then the absorbance was measured at 450 nm. For the colony formation assay, a total of 1x103 cells/well was seeded into 6-well plates and cultured for 14 days in 10% FBS medium at 37 °C. The colonies were fixed with 4% paraformaldehyde and stained with 0.5% crystal violet (Beyotime, China). For apoptosis analysis, cells (1x106/ml) from different treatment groups were digested with trypsin without EDTA, washed with ice-cold PBS, and centrifuged at 2000×rpm for 5 min, followed by resuspension in binding buffer. Subsequently, the cells were incubated with Annexin-V and PI (Solarbio, China) for 25 min at 4 °C in the dark. Then, the stained cells were analyzed using DxP Athena™ (Cytek Biosciences, USA), and the percentage of Annexin V+ PI- and Annexin V+ PI+ cells was calculated as the apoptosis rate. For cell cycle analysis, 70% icy ethanol was used for cell fixation at 4 °C overnight. After staining with propidium iodide (PI) (Solarbio) and RNase (Invitrogen), the percentage of cells in G1, G2, and S phases was analyzed by DxP Athena™ (Cytek Biosciences, USA).
In vivo experiments
Four-week-old NOD/SCID mice were obtained from SJA Laboratory Animals (Hunan, China). SKOV3 or A2780 cells infected with the indicated lentiviral vectors were suspended in 100 μl mixed liquid PBS and Matrigel and subcutaneously injected into the right armpit of NOD/SCID mice at the age of 5 weeks. After 28 days, the animals were sacrificed and used for measurement and immunohistochemistry staining. The tumor volume was calculated using the following formula: V (mm3) = 0.5 × length (mm) × width2 (mm2).
RNA-seq and bioinformatic analysis
Total RNA was isolated from A2780 cells after infection with shNC and shNCAPG virus using RNAiso Plus reagent (Takara, Japan). RNA libraries were prepared according to the manufacturer's instructions for the TruSeq RNA Sample Prep Kit (Illumina, USA). HISAT2 software was used to map all clean reads of mRNA to the UCSC hg38 primary assembly genome. Differential gene expression analysis and bioinformatics analysis were conducted in R. DEGs between the samples were identified using the Bioconductor package DESeq2. We considered a gene differentially expressed when it met the thresholds of |log2 Fold change| ≥ 1.5 and p < 0.05. Subsequently, functional enrichment analyses were conducted by Metascape (https://metascape.org/) and Gene Set Enrichment Analysis (GSEA) (www.gsea-msigdb.org).
Statistical analysis
The 2-tailed Student t test was used for comparisons between two groups, and one-way analysis of variance (ANOVA) was used for multiple-group comparisons. Data were plotted using GraphPad Prism 6.0 software. Statistical analyses were carried out with SPSS software. Correlations were analyzed by Pearson correlation. P < 0.05 was considered significant.