2.1 Cell culture
Normal human immortalized urothelial cell line SV-HUC-1 and the human BCa cell lines T24, 5637, RT4, UM-UC-3, SW780 and TCCSUP were purchased from the American Type Culture Collection (ATCC, Manassas, VA). T24, 5637 and SW780 were cultured in RPMI-1640 medium. UM-UC-3 and TCCSUP were cultured in DMEM. RT4 was cultured in Mcoy’s 5a, and SV-HUC-1 was cultured in F-12K medium. 10% fetal bovine serum (FBS; Biological Industries, Beit Haemek, Israel) and 1% penicillin/streptomycin (GIBCO, Gaithersburg, MD, USA) were added to get complete growth medium.
2.2 BCa specimens
All BCa samples were collected from the Peking University Shenzhen Hospital and Shenzhen University Nanshan Hospital. The study was approved by the Ethics Committee of Shenzhen University Nanshan Hospital with written informed consent obtained from all patients. The pathological status of the specimens was provided by the board-certified pathologist.
2.3 Western blot
Protein extracts were prepared in RIPA Lysis Buffer (#P0013B; Beyotime), supplemented with PMSF, protease inhibitor and phosphatase inhibitor cocktail. Protein concentrations were determinated using Bicinchoninic Acid Kit (Sigma-Aldrich) according to the manufacturer’s protocol. Cell lysates were resolved by SDS-PAGE and transferred onto PVDF membranes. Membranes were blocked for 1 hour with 5% non-fat milk in TBST (Trisbuffered saline containing 0.1% Tween 20) and incubated overnight at 4 °C with primary antibodies and required secondary antibodies conjugated to horseradish peroxidase and developed by chemiluminescent substrates.
2.4 RT-qPCR and ChIP
Total RNA was extracted using TRIzol™ Reagent (Invitrogen) and purified using RNeasy Mini Columns (Qiagen), according to the manufacturer’s protocol. For mRNA and lncRNA MIR497HG detection, cDNA was generated using SureScript™ First-Strand cDNA Synthesis Kit (genecopoeia). Quantitative PCR was then performed using the SYBR Green qPCR MasterMix (Takara). To analyze miR-195 and miR-497 expression, cDNA was synthesized by a mir-X miRNA First-Strand Synthesis Kit (Takara,Dalian, China). MiRNA expression were used mir-X miRNA qRT-PCR SYBR Kit (TOYOBO, Osaka, Japan) according to the manufacturer’s instructions, with U6 as the control.
2.5 Chromatin immunoprecipitation (ChIP)
Chromatin immunoprecipitation (ChIP) assays were performed according to manufacturer’s instructions using Cell Signaling Immunoprecipitation Kit (#9002). Briefly, 5637 cells were fixed paraformaldehyde and lysed in Buffer A supplemented with DTT, Protease Inhibitor Cocktail (PIC), and PMSF, and incubated on ice for 10 min. Nuclei were pelleted and resuspended in Buffer B + DTT. DNA was digested with 0.5 ul Micrococcal Nuclease. Nuclei were again pelleted, resuspended in ChIP buffer + PIC and PMSF, and incubated at 4 °C. The lysates were clarified by centrifugation and ChIP was carried out by incubating the sample with Rabbit IgG or E2F4 antibody (Abcam), followed by immobilization on protein A/G-agarose beads (Life Technologies). The chromatin was eluted from Antibody/Protein G Agarose Beads, cross-links were reversed, and DNA was purified using spin columns. The qPCR was performed using MIR497HG promoter or GAPDH primers. Ct values were normalized to input DNA. The detailed primer sequences for RT-qPCR and ChIP assays are listed in supplementary Table S1.
2.6 Cell Counting Kit-8 (CCK-8) assay
Cells were cultured in 96-well plates at a concentration of 3 × 103 cells per well. After treatment, 10 µl CCK-8 reagent (Dojindo, Kumamoto, Kyushu, Japan) was added to each well to react for 0.5 h. The absorbance was measured at 450 nm using a microplate reader.
2.7 Colony formation assay
1000 cells/well were plated onto six-well plates, which were incubated at 37℃ and 5% CO2 until colonies were formed. After 10–15 days, colonies were fixed using 0.05% crystal violet in 4% paraformaldehyde and counted using Image J program.
2.8 Cell migration assay
Cells were seeded in six-well plate (5 × 105/per well) and incubated at 37 °C in a humidified incubator containing 5% CO2 to get 100% confluence before transfection. A clear line was created by scratching with a sterile 200 µl pipette tip. Images were taken from each well quickly. After 24 hours, pictures were taken again with the help of a digital camera system. Migration distance was calculated at the time of 0 and 24 h. Experiments were performed at least three times.
2.9 Cell invasion assay
Cells were transfected with siRNAs/plasmids for 48 h and then trypsinized and resuspended in serum-free medium. A total of 1 × 105 cells were then added to the upper chambers of the Transwell inserts (Millicell; Merck KGaA) and allowed to migrate toward the bottom of the chambers. After 24 h, the remaining cells in the upper chamber were removed, and cells on the underside were fixed in 4% paraformaldehyde for 30 min at room temperature, stained with 0.1% crystal violet for 30 min at room temperature and captured using an Olympus type light microscope sz30. Quantification of the migrated cells was performed by counting cell numbers.
2.10 Plasmids, lentiviral production and transfection
YAP1 and SMAD3 coding sequence was cloned into pCMV-HA-N expression vector (SalI/BglII and KpnI/NotI). The primer sequences used for clone are provided in supplementary Table S1. pLemiR control, pLemiR-195 or pLemiR-497 plasmid were packaged with pMDL,VSVG and pRSV-Rev into HEK-293T cells. To establish stable cell lines, the concentrated lentivirus were directly added into cancer cells and incubated at 37 °C for 48 hours before they were washed out PBS. Finally, cells were selected with 2.5 mg/mL puromycin for 4 days. For luciferase reporter assay, the 3’ UTR fragments of YAP1, SMAD3,CCND1 and BIRC5 containing the wild-type or mutant miR-497 ~ 195 cluster putative target sites were directly synthesized from GeneCreate (Wuhan, China), and cloned downstream of the Renilla luciferase cassette in psiCHECK-2 (Promega);The CTGF-luc plasmids were generated as described previously [29]. The promoter fragments of human MIR497HG were directly synthesized from GeneCreate (Wuhan, China), and cloned into pGL3-Basic vector (Promega). A site-directed mutagenesis kit (Thermo Fisher Scientific) was used to mutate the miR-497 ~ 195 cluster or E2F4 binding sites of these vectors. The primer sequences used for the site-directed mutagenesis are provided in supplementary Table S1. All sequences were confirmed by sequencing.
The miRNA inhibitors and mimics of miR-ctrl, miR-195 and miR-497 were obtained from Ribobio (Guangzhou, China). The indicated cancer cells were transfected with 50 nM of mimic or inhibitor of miR-ctrl, miR-195 and miR-497 using Lipofectamine 3000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. The expression levels of miR-195 and miR-497 were quantified after 48 h transfection.
2.11 Luciferase reporter assay
For 3’ UTR luciferase reporter assays, miR-497 or miR-195 mimic or control mimic (Ambion) and indicated psiCHECK-2-3’ UTR wild-type or mutant plasmids were co-transfected into T24 or 5637 cells cultured in 24-well plates using lipofectamine 3000 (Thermo Fisher Scientific). Renilla and firefly luciferase activities were measured with the dual-luciferase reporter assay system (Promega, Madison, WI, USA) according to the manufacturer’s manual.
For luciferase reporter assay, in order to measure promoter activities, the MIR497HG promoter fragment was inserted into pGL3-basic plasmid, named pGL3-MIR497HG. Then pcDNA3.1-E2F4 expression plasmid or empty vector control and pGL3-MIR497HG or pGL3-MIR497HG-mut were co-transfected into T24 or 5637 cells cultured in 24-well plates using lipofectamine 3000 (Thermo Fisher Scientific). The firefly and Renilla luciferase activity was measured after 24–48 h with the dual-luciferase reporter assay system (Promega). Firefly luciferase activity was normalized to Renilla activity.
2.12 Statistical analysis
Statistical analysis was performed by the SPSS 20 (SPSS Inc., Chicago, IL, USA). Two-tailed unpaired or paired Student’s t test, ANOVA (Dunnett’s or LSD post hoc test) and Pearson correlation coefficients were used according to the type of experiment. Kaplan-Meier method was used to estimate survival curves, which were compared using the Log-rank (Mantel-Cox) test. The statistical significance between data sets was expressed as P values, and P < 0.05 was considered significant; * (p < 0.05), ** (p < 0.01), *** (p < 0.001).