Clinical specimens
All prostate cancer and pared adjacent non-cancerous specimens were collected from patients who underwent radical prostatectomy at the Department of Urology of the First Affiliated Hospital of Nanjing Medical University from 2010 to 2013. No other treatment, such as hormone therapy, chemotherapy or radiotherapy, was used prior to radical prostatectomy. Also the detail information of those patients was obtained. Appropriate informed consent was provided to the patients and the study was approved by the Institutional Ethics Committee of the First Affiliated Hospital of Nanjing Medical University (China). 20 pairs of tissues were used to perform quantitative RT-PCR analyses and 6 pairs were used to perform western blot.
Immunohistochemistry (IHC)
52 pair of prostate cancer tissues and adjacent non-cancerous tissues were stained with anti-WTAP antibody (1:1000, Cell signal technology). Standard staining protocols were used. Positive reactions were defined as showing brown signals in the cell cytoplasm and were scored for scoring staining intensity (SI) and the percentage of positive cells (PP). SI was scored on a scale of 0 to 3. 0 score represents a negative stain; 1 score represents a weak stain; 2 score represents a moderate stain; 3 score represents a strong stain. PP was scored into five categories: 0 (<5% positive cells), 1 (5% to 25 %), 2 (26% to 50%), 3 (51% to 80%) or 4 (> 80%). The final score was calculated by multiplying SI and PP score. Each component was scored independently and summed for the results. Two urologists scored the positive level of immunohistochemical staining and patients were divided into two groups by the final score: weak- (0-7) group and strong-staining (8-12) group.
Cell lines and culture conditions
Human prostate cancer cell lines (PC3, DU145 and LNCaP) and human prostatic epithelial cells (RWPE.1) were purchased from the Institute of Biochemistry and Cell Biology of the Chinese Academy of Sciences (Shanghai, China). Human prostate cancer cell lines were cultured in F-12K, DMEM or RPMI 1640 (Gibco, USA) medium supplemented with 10 % fetal bovine serum (BI, Israel) and 100 U/mL penicillin (Gibco, USA) in humidified air at 37 °C with 5 % CO2 incubator. Human prostatic epithelial cells (RWPE.1) were cultured in K-SFM with 0.05mg/ml BPE, 5ng/ml EGF and 1% P/S (Gibco, USA).
Plasmid construction and lentivirus packaging
Cells were stably transfected with lentivirus containing the WTAP overexpression (WTAP), WTAP knockdown (shWTAP), a scramble control (SCR) or a negative control (NC) which was an empty lentiviral vector, following the manufacturer’s instructions. All plasmids were verified by sequencing (Novobio, Shanghai, China). Cells were plated in 6 wells dishes at 30%~ 50% confluences and infected with the retroviruses. Meanwhile, polybrene (5 μg/ml) was added with the retroviruses to enhance the target cells infection efficiency. Cells were then co-cultured with puromycin(3 μg/ml) for 1-2 weeks and stable transfected cells were selected. CDK4 siRNA (5′-GCAUGUAGACCAGGACCUATTUAGGUCCUGGUCUACAUGCTT-3′) and negative control were obtained from GenePharma (GenePharma, China). Lipofectamine 3000 kit (Invitrogen, USA) was used for transfection according to the manufacturer’s instructions.
RNA extraction and quantitative RT-PCR analyses (qRT-PCR)
Total RNA was extracted from tissues or cultured cells with TRIzol reagent (TaKaRa,) and cDNA was synthesized using Primescript RT Reagent (TaKaRa) according to the standard manufacturer’s protocols. Quantitative RT-PCR analyses were performed using a protocol from fluorescent SYBR Green I methodology (Takara) on an ABI StepOne Plus instrument (Applied Biosystems, Carlsbad, CA, USA) and in a total reaction volume of 10 μl which includes 5 μl of SYBR Premix (2x), 3 μl of DEPC water, 1 μl of cDNA solution, 0.4 μl of PCR forward primer solution (10 μM), 0.4 μl of PCR reverse primer solution (10 μM) and 0.2 μl of ROX Reference Dye I (50x). The relative quantitative value was expressed by the 2−ΔΔCt method. Each experiment was performed in triplicates and repeated three times. The PCR primers were showed in Supplementary Table S1.
Cell proliferation assays
Cell proliferation was assessed by CCK-8 assay (Dojindo, Japan) according to the manufacturer’s instructions. Cells were diluted to 2000 cells per wells with medium and seeded in a 96-well plate. After cultured for 24, 48, 72, 96 and 120 h at 37°C, spent medium was replaced with 100 ul fresh medium containing 10% CCK-8 and incubated at 37°C for 1 h. The absorbance was finally determined at 450 nm using a microplate reader (Thermo Scientific, USA).
Colony formation assays
Cells were trypsinized into single-cell suspension. 600 cells were plated into 6-well plate and maintained in media containing 10% fetal bovine serum (FBS) for 10-20 days. Then colonies were fixed with methanol and stained with crystal violet (Beyotime, Beijing, China) after washed by phosphate-buffered saline (PBS), Visible colonies were manually counted after dried at room temperature. Three parallel plates were measured in each treatment group.
Cell migration/invasion assay
Cells (2.0 ~4.0× 104) were suspended in 200 μl with serum-free medium and seeded in the top chamber of the transwell (Millicell, US) which was coated with or without Matrigel (BD Biosciences, USA) for the invasion and migration assays. Culture medium containing 10 % FBS was placed in the bottom chamber. Cells were incubated for 24, 48 or 72 h at 37 °C. The cells that did not migrate through the membrane were manually wiped out with a cotton swab. Cells which passed through the filter were stained using 0.1 % crystal violet after being fixed with methanol. Images of five random fields (200×) were captured from each membrane. And then the number of migratory or invasive cells was counted. Each experiment was performed in triplicate.
Western blotting analysis
Cells were lysed by using the mammalian protein extraction reagent RIPA (Beyotime, Beijing, China). Protein was separated by 10 % sodium dodecyl sulfatepolyacrylamide gel electrophoresis (SDS–PAGE) and then transferred to polyvinyli denedifluoride membranes (PVDF, Milipore, USA). After blocked with 5% skim milk in Tris-buffered saline with 0.1% Tween 20 (TBST) for 2 h at room temperature, the membranes were incubated for one night at 4°C with β-actin (1:1000, Cell signal technology, USA), GAPDH(1:1000, Cell signal technology, USA), β-catenin (1:1000, Cell signal technology, USA),CDK4 (1:1000, Cell signal technology, USA), CDK6 (1:1000, Cell signal technology, USA), CDK2 (1:1000, Cell signal technology, USA), MMP2 (1:1000, Cell signal technology, USA), MMP9 (1:1000, Cell signal technology, USA) or WTAP (1:1000, Abcam,USA) antibodies. The secondary antibody was horseradish peroxidase- conjugated goat anti-mouse-IgG (1:1000, Cell signal technology, USA) or anti-rabbit-IgG (1:1000, Cell signal technology, USA). Enhanced chemiluminescence chromogenic substrate was used to visualize the bands, and the intensity of the bands was quantified by densitometry (Quantity One software; Bio-Rad, USA).
RNA stability
PC3 or LNCaP cells lines were treated with 4ug/ml actinomyclin D (Act D) for 0, 1, 2, 4, 6 or 8 h. Total RNAs were extracted and used to generate cDNA. And then qRT-PCR was performed. The level of CDK4 transcript was normalized to β-actin and the relative half-life of CDK4 was calculated.
Dual-luciferase reporter assay
Dual-luciferase reporter assay was performed according to manufacturer′s protocol(Promega, USA). The full length wild type CDK4 3’-UTR (wt) and mutant CDK4 3’-UTR (mut) was inserted into the pLenti-UTR-Luc vector (Promega, USA) and Renilla luciferase vector (pRLCMV; Promega, USA) was used as an internal control. The reporters were then transfected into PC3 and LNCaP WTAP overexpression cells (WTAP) and the control cells (NC) using Lipofectamine 3000 reagent (Invitrogen USA). After 48 hours of transfection, the luciferase activity was detected by Dual-Luciferase Reporter Assay System (Promega, USA). Renilla luciferase activity was normalized against Firefly luciferase activity.
RNA immunoprecipitation (RIP)
RNA immunoprecipitation was performed by using Magna RIP RNA-Binding Protein Immunoprecipitation Kit (Millipore, USA) according to a standard protocol. Prostate cancer cells were lysed by RIP lysis buffer. Cell lysates were immunoprecipitated with anti-WTAP antibody or non-immunized IgG at 4 ℃ overnight, followed by RNA purification. Then RT-PCR and qRT-PCR were used to measure the expression level of CDK4 transcript in the WTAP or IgG immunocomplexes.
Tumorigenesis in nude mice
BALB/C male nude mice (4-6-weeks old, 18–22 g) were randomly divided into two groups and each containing 4 mice. Stabled WTAP-knockdown PC3 cells or scramble control cells (1 × 106 cells in 0.15 ml PBS) was subcutaneously injected into the mice and the growth of tumors was followed up for 4 weeks. Tumor volume was measured using a caliper per 1 week. After 4 weeks, mice were sacrificed and measured for final tumor size. Mouse studies were conducted according to the Guide for the Care and Use of Laboratory Animals and approved by the Animal Care and Use Committee of Nanjing Medical University.
Statistically analysis
All data were expressed as mean ± SD (standard deviation), and analysis were performed using SPSS version 17.0 software (IBM). A Student’s t test or a chi-square test was used as appropriate. Patient survival was evaluated by the Kaplan-Meier method and compared by the log-rank test. Values of P < 0.05 were considered statistically significant.