Cell culture and treatment
Human ovarian cancer cells (SKOV3 and A2780) were obtained from the Cell Bank, Shanghai Institute of Biochemistry and Cell Biology (Shanghai, China). The cisplatin-resistance cell line (SKOV3-DDP and A2780-DDP) were established in our lab. All cell lines were cultured in RPMI medium 1640 medium (Gibco) supplemented with 10% (v/v) fetal bovine serum (FBS, Gibco),100 µg/ml streptomycin, and 100 U/ml penicillin in a humidified atmosphere at 37°C with 5% CO2. For cisplatin treatment, ovarian cancer cells were cultured with 10–80 µM cisplatin (selleck) for 48 h. For autophagic promotion and inhibition, cells were treated with autophagic antagonist-chloroquine (50 µM, sigma) and autophagic agonist-rapamycin (100 nM, sigma), respectively.
qRT-PCR
Total RNA from tissues and cultured cells was extracted using TRIzol reagent(sigma). RNA concentration was measured and equal amount of mRNA and miRNA was reverse transcribed to cDNA using reverse transcription kits(Takara and TransGen) respectively. Quantitative realtimePCR (qPCR) was performed on ABI 7500 real-time PCR system using specific primers as following: YES1 forward primer: 5′-CTCAGGGGTAACGCCTTTTGG-3′; reverse primer: 5′-CACCACCTGTTAAACCAGCAG-3′; GAPDH forward primer: 5′-GGAGCGAGATCCCTCCAAAAT-3′; reverse primer: 5′-GGCTGTTGTCATGCTTCTCATGG-3′; miR-133a forward primer: 5′-CAGCTGGTTGAAGGGGACCAAA-3′; U6 forward primer: 5′-CTCGCTTCGGCAGCACA-3′; reverse primer: 5′-AACGCTTCACGAATTTGCGT-3′. GAPDH and U6 were used as internal control. Relative YES1 expression was normalized to GAPDH levels and relative miR-133a was normalized to U6 levels both using the 2−ΔΔCt quantification method.
YES1 and miR-133a transfection
YES1-Overexpression (YES1-OE) vectors and a negative control and miR-133a mimics, miR-133a inhibitor and relative controls were purchased from Yazai Biotechnology Co Ltd. (Shanghai, China). The siYES1 and relative controls were purchased from Gene Pharma (Shanghai, China). Transfection was conducted using Lipofectamine 3000 according to the manufacturer’s manual. Lentiviruses-YES1-OE for stable overexpression of YES1 or the negative control construct was designed and constructed by Hanbio Biotechnology Co., Ltd. (Shanghai, China).
Western blot analysis
Tissue samples or cultured cells were lysed, and the protein concentration was measured by the BCA protein assay. Equal amounts of protein were resolved by 10% or 15% SDS-PAGE and transferred onto a PVDF (Polyvinylidene fluoride) membrane. The membranes were blocked at room temperature with 5% skimmed milk and then incubated with primary antibodies overnight at 4°C. After washing with TBST (tris buffered saline tween), the membranes were further incubated with fluorescent secondary antibodies at room temperature in the dark for 1–2 h. GAPDH was used as internal control. The signals were detected using an Odyssey detection system (Odyssey CLx, LI-COR biosciences, NE, USA). Quantification analysis of western blot was performed using software ImageJ (Bethesda, USA). Primary antibodies against YES1 (1:1000, ABclonal, A0628), LC3b (1:1000, Abcam, AB192890), Gapdh (1:5000, Proteintech, 51067-2-AP).
Cell proliferation
Cell proliferation was determined by Cell Counting Kit-8 assay (CCK-8)( Dojindo Laboratories, Kumamoto) according to the manufacturer’s protocol. SKOV3 and SKOV3-DDP cells were seeded at a density of 3 × 103 cells/well and A2780 and A2780-DDP cells were seeded at a density of 8 × 103 cells/well into a 96-well plate. 10 µL CCK-8 working solution was added and cells were incubated for 2 h before the measurement of absorbance at 450 nm.
Luciferase reporter assays
WT or mutated 3′-UTR of YES1 sequences were cloned and constructed into the pGL3-Luc reporter vector. A2780 was transfected with the WT or mutated luciferase reporter vectors, together with miR-133a mimics or negative control. Relative luciferase activity was analyzed using a Dual-Luciferase Reporter Assay Kit 48h later.
GFP-RFP-LC3 assay
To monitor the autophagy, the tandem GFP-RFP-LC3 adenovirus construct obtained from Hanbio Inc (Shnaghai, China) which capitalizes on the pH difference between the acidic autolysosome and the neutral autophagosome and the pH sensitivity differences exhibited by GFP (green fluorescent protein) and RFP (red fluorescent protein) to monitor progression from the autophagosome to autolysosome was used. In brief, A2780 and A2780-DDP cells were infected with tandem GFP-RFP-LC3 adenovirus for 2 h and then were cultured with normal medium and 10 µM cisplatin for 48 h. Finally, cells were treated and imaged for GFP and RFP by using fluorescence microscopy.
The international cancer genome consortiu(ICGC)dataset analysis
The RNA sequencing data of ICGC OV-AU used for gene expression analysis. Genes with low read abundance were filtered, followed by the rlog transformation based on the R package DESeq2 (version 1.28.1). Then the principal component analysis (PCA) of the normalized expression matrix, relied on the FactoMineR package (version 2.3), was performed to detect the outlying samples. The remaining samples were randomly divided into primary sensitive (n = 12) and relapse resistant (n = 24) groups from 23 high-grade serous ovarian cancer ( HGSOC) patients [15].
In vivo tumorigenicity
All the mice experiments were approved by the Experimental Animal Ethics Committee of the Tenth people's Hospital Affiliated of Tongji University. Female BALB/c nude mice (4–5 weeks old, 18–20 g) were purchased from Vital River Laboratory (Beijing, China). For xenograft model, 5 × 106 of A2780 ovarian cancer cells transfected with Lentiviruses-YES1-OE or the negative control were subcutaneously implanted into nude mice. Intraperitoneal injection with density of 5mg /kg cisplatin was conducted every 3 days in a week after all the tumor nodules in the same group were appeared. Tumor volume was calculated based on tumor sizes determined by a vernier caliper every week (length × width2/2). The mice were euthanized 14 days later and tumor weights were determined.
Statistical analysis
All statistical analyses were conducted using a SPSS software (version23.0) and GraphPad Prism 6. Experimental results were presented as the mean ± standard deviation of the mean (SD) based on the results from three independent experiments. Unpaired two-tailed Student’s t-test and the one-way analysis of variance (ANOVA) were used where necessary for calculation of p values. Differences in clinical pathological factors between the YES1 high- or low-expression groups were analyzed via the Chi-square test. P values < 0.05 was considered statistically significant.