Identification of BC associated genes
The expression datasets for genes in bladder tissues of BC patients and normal bladder tissues were obtained from the GEO databases (GSE13507 and GSE40355) and the Cancer RNA sequencing (RNA-Seq) Nexus database. To obtain more accurate results, the differentially expressed genes were obtained based on the intersection of the three databases. Differential expression analysis was performed between the normal colon and BC tissues using a t-test with False Discovery Rate (FDR)-adjusted P-value less than 0.05.
Next, the seven intersected RNAs obtained from the intersection of GSE40355, GSE13507 and the Cancer RNA-Seq Nexus database, in addition to the six STAT genes including STAT1, STAT2, STAT3, STAT4, STAT5B and STAT6 genes, were analyzed for survival analysis. Survival analysis was performed with Kaplan-Meier survival curves on the website of http://kmplot.com/analysis/index.php?p=service.
Cell culture
The human BC cell lines (5637, T24, J82, EJ and RT4) and normal bladder uroepithelial cell line SV-HUV-1 were purchased from the Shanghai Institute of Cell Biology, Chinese Academy of Sciences (Shanghai, China). Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; Invitrogen, Carlsbad, CA, USA) containing 10% fetal bovine serum (FBS; Gibco, Thermo Fisher Scientific, Waltham, MA, USA), 1 mmol/L glutamine, and 100 U/mL penicillin at 37°C in an incubator with 5% CO2. The expression of lncRNA PVT1 and STAT5B in the above cells was examined in pre-experiments, and the T24 and EJ cell lines with the highest lncRNA PVT1 and STAT5B expression levels were selected for the formal experiments.
Western blot (WB) and antibodies
Cell lysates were separated by 10% sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and transferred to nitrocellulose membranes (GE Healthcare, USA). The membrane was blocked with 5% skim milk for 2 h at room temperature in TBS (20 mM Tris-HCl, 137mM NaCl, pH 7.6), and incubated overnight at 4°C with specific primary antibodies, followed by the secondary antibodies at room temperature for 2 h. WB analysis was performed using the Bio-Rad Western blotting system (Bio-Rad, USA). β-actin was used as an internal control. The specific antibodies used for WB were as follows: anti-STAT5B (phospho Y705) antibody (EP2147Y, ab76315) and anti-STAT5B antibody (E121-21, ab32500).
Quantitative real time polymerase chain reaction (qRT-PCR)
Total RNA was extracted from samples using Trizol reagent according to the manufacturer’s protocol instructions (Invitrogen, CA, USA). Approximately 30 mg of each sample was grinded thoroughly with a homogenizer. After centrifugation and the treatment of Trizol and chloroform, the upper suspension was removed, and the RNA precipitate was washed with 1 mL of 75% ethanol. RNase-free water was added to the dried RNA precipitate to dissolve the RNA completely. qRT-PCR was performed with SYBR® Premix Ex Taq™ II kit (RR820A, TaKaRa, Dalian, China) in ABI 7500 Real Time PCR System (ABI Company, Oyster Bay, NY, USA). All samples were done in triplicate and normalized by the housekeeping gene glyceraldehyde 3-phosphate dehydrogenase (GAPDH). The primer sequences used for qRT-PCR and promoter were listed in Table 1.
Immunohistochemistry (IHC)
The paraffin-embedded tissues sections were dewaxed in xylene and rehydrated in ethanol gradient. Then the tissues were incubated in 1% hydrogen peroxide and boiled in citrate buffer (10mM, pH = 6.0) for 15min. Later, following incubation with the primary antibodies at 4°C overnight, horseradish peroxidase (HRP)-conjugated goat anti-rabbit secondary antibodies (zsbio, Beijing, China) were used for incubation with the tissues. IHC staining was conducted with triplicate sections for each sample.
Immunofluorescence (IF)
Deparaffinization and rehydration were performed following standard procedures using xylene and graded solutions. Tissues were then blocked with Protein Blocking Solution (Dako) and incubated for 60 min at room temperature followed by incubation with antibodies. The images were obtained with fluorescence microscope (Olympus) and measured using ImageJ 2.0 software. IF staining was conducted with triplicate sections for each sample.
Fluorescence in situ hybridization assay (FISH)
To identify the subcellular localization of lncRNA PVT1 in BC cells, FISH assay was conducted using a FISH kit (Ribo Bio, Guangzhou, China) in accordance with the manufacturer’s instructions. The cells were fixed with 4% paraformaldehyde and treated with 0.5% Triton in PBS. After pre-hybridization, they were then hybridized at 5 μM probe concentration overnight. Ribosomal RNA (18S) was used as the reference gene. Streptavidin-biotin system labeled PVT1 RNA probe was used as the probe mix. Samples were visualized by a confocal microscope (Zeiss).
Cell counting test
Cell counting test was performed to detect cell proliferation using Cell Counting Kit-8(CCK-8) (Beyotime, Shanghai, China). Each well (96-well plate) was filled with approximately 1 × 105 cells in a culture volume of 100 μL. Each group was set with 3 parallel wells for the assay. Cell-free wells with complete medium and CCK-8 solution were set as background control wells. A total of 10 μL CCK-8 solution was added, followed by incubation for 1h. Mix it thoroughly and the absorbance was measured at 50 nm.
Wound healing assay
Wound healing assay was performed to detect cell migration. Approximately 1×105 cells/mL were added to each well and cells grew to more than 90% the next day. Cell scratch wounds were created using a sterile 20 μL pipette tip, after which the dislodged cells were washed out with fresh medium. Wound healing was assessed at 0 h and 48 h by measuring the wound areas on digitized photographs using ImageJ software. The wound healing assay was performed in triplicate.
Invasion assay
The invasion assay was performed using transwell membranes precoated with DMEM-diluted Matrigel® (BD Biosciences) for 2 h at 37°C. About 2×104 Cells were seeded into the upper chamber in serum free medium in triplicate. A total of 500 µL DMEM/F-12 medium supplemented with 10% FBS was plated in the lower chambers. Cells were allowed to migrate towards the lower chamber. After 72 hours, the invasive cells were fixed in methanol for 15 min at room temperature and were stained using hematoxylin for 10 min. The invasion was examined with light microscopy according to the manufacturer’s protocols.
RNA immunoprecipitation (RIP) assay
RIP assay was performed using EZ-Magna RIP™ RNA-Binding Protein Immunoprecipitation Kit (Catalog No. 17-701) (Millipore, Burlington, MA, USA) according to the instructions. Briefly, cell lysates were collected and incubated with magnetic beads conjugated with antibodies. RIP was performed using either anti-SNRNP70 (Cat. # CS203216) or Normal Rabbit IgG (Cat. # PP64B) as the immunoprecipitating positive or negative antibody. The relative abundance of lncRNA PVT1was normalized to the amount of enriched U1 snRNA (Cat. # CS203215) via qRT-PCR.
RNA pull-down assay
RNA pull-down assay was performed using the PierceTM Magnetic RNA-Protein Pull-Down Kit (Thermo Fisher Scientific, Waltham, MA, USA). Briefly, the cell lysates were incubated with control or biotinylated lncRNA PVT1 at room temperature for 4 h, followed by the addition of streptavidin magnetic beads (Thermo Fisher Scientific, Waltham, MA, USA) at 4°C for 60 min with rotation. After three washing steps with washing buffer, the RNA-binding proteins were eluted using 50 μL elution buffer and analyzed via WB. The BIO-PVT1 probe sequence was designed by the prediction of catRAPID fragments for a possible PVT1-STAT5B binding interval of 40-119bp. BIO-PVT1 probe sequence was: 5'-GTCCCGGGGCACATCTTTGCTCGCAGCTCGTCGT-3'.
si-RNA and overexpressed plasmid construction
si-RNA transfection was performed using Lipofectamine™ 3000 Reagent. Dilute 7.5 μL reagents and si-RNA with 125 μL Opti-MEM® I. Mix the diluted siRNA with reagents and incubate for 5 minutes at room temperature. Add them to each well containing cells and culture medium. And then gently mix it up and incubate for 4 hours at 37°C. The target sequence for si-PVT1 #1 was 5’-GAGCTGCGAGCAAAGATGT-3’, and for si-PVT1 #2 was 5’-ACTTTAAGTGGAGGCTGAATCATCT-3’. The target sequence for si-STAT5B was 5’-GTGTCAAGGCAGATTAGTTAT-3’. Overexpressed plasmids were performed using Lipofectamine™ 3000 Reagent. Dilute 7.5 μL reagents and 5 μL plasmid reagents with 125 μL Opti-MEM® I. Mix the diluted plasmids with reagents and incubate for 5 minutes at room temperature. Add them to each well containing cells and culture medium. And then gently mix it up and incubate for 4 hours at 37°C.
Cell transfection
Using a lentiviral system, stably transfected cells were created. Lentiviral vectors encoding the human STAT5B gene and lncRNA PVT1 and its siRNAs, or empty vector were transfected into T24/EJ cells with a multiplicity of infection of 40 to 50 in the presence of polybrene (5 μg/mL). Transfected cells were selected at 48 h after transfection. Transfection efficiency was confirmed by qRT-PCR. Pooled populations of knockdown cells and overexpressed cells, which were obtained 2 weeks after selection without subcloning, were used in both in vitro and in vivo experiments.
Luciferase reporter assay
Wild-type or mutant lncRNA PVT1 promoter plasmids were cotransfected into T24/EJ cells with STAT5B overexpressed plasmids to detect the effect of STAT5B on the activation for lncRNA PVT1 promoter. The high scoring predicted lncRNA PVT1-STAT5B binding sites was 5’- ATTTCACTGAA -3’ of 1532-1542bp. T24/EJ cells were plated at a density of 2 × 104 cells per well in 24-well plates for 24 h. After incubation, 4 μg of plasmids were transfected into T24/EJ cells. The cells were collected after about 48 h in culture for luciferase reporter assays using the Dual-Luciferase® Reporter (DLR™) Assay System (Promega) according to the manufacturer’s instructions. A fluorescence signal was generated by the addition of Photinus pyralis and the signal lasted for 1 min. After quantifying the fluorescence intensity, the Stop & Glo® reagent was added to quench the above reaction and simultaneously initiate the Renilla reniformis reaction, while a second measurement was performed. The luciferase activity was determined by the relative light unit value of the two measurements. The assay was performed in triplicate.
Chromatin immunoprecipitation (ChIP)
ChIP assay was performed using the EZ-ChIP™ Kit (Millipore). Firstly, break up the DNA by sonication on crushed ice and centrifuge at 4°C at 12,000 rpm for 10 min. Then remove the precipitates and leave the supernatant. Take 100 μL of chromatin solution from the previous step. Add 900 μL of dilution and 60 μL of Protein G Agarose to each tube. After incubation at 4°C for 1h and centrifugation at 3000 rpm for 1 min, add IP antibody to supernatant and set up each control as follows: positive control: anti-RNA polymerase; negative control: normal rat IgG. After incubation overnight at 4°C and adding Protein G Agarose to per tube, wash it with Wash Resuspend and Wash Buffer. Then add 5 M NaCl and incubate at 65°C for 4-5 h to release the Protein/DNA crosslink. Finally, add sample/Bind Reagent to purify the DNA.
DNA-affinity Precipitation Assay (DAPA)
Based on the high scoring predicted lncRNA PVT1-STAT5B binding sites 5’- ATTTCACTGAA -3’ of 1532-1542bp, we designed 5’-biotinylated-wt-Sense oligonucleotide and the Anti-sense oligonucleotide for DAPA to detect STAT5B expression levels. Briefly, following annealing of Sense and Anti-sense oligonucleotdies for 1 h at 95°C, 4 μg of annealed biotinylated probe was incubated with 500 μg of nuclear cell lysate, and 40 μL of streptavidin-agarose bead was suspended in diluted PBS for 2–3 h rocking at room temperature. The streptavidin-agarose beads were pelleted by centrifugation and washed 5 times with PBS. The captured probe-binding proteins were eluted from the streptavidin-agarose beads by boiling in 2×SDS sample buffer for 5 min and subjected to immunoblot analysis.
Nude mice tumorigenesis
Every experimental group had 4 mice. Male BALB/c nude mice (4-6 weeks of age) were injected with 1×106 cells in a total volume of 0.2 mL per injection site selected subcutaneously near the extremities. Tumor sizes were measured according to the longest diameter (a) and shortest diameter (b) after feeding nude mice every 3 days for 6 consecutive times until the tumor was visible to the naked eyes (about one week). Tumor growth curves were plotted using time as the horizontal coordinate and tumor volume as the vertical coordinate. Tumor tissues were taken and photographed for IHC testing. Tumor volume was calculated according to the formula: V = a × b2 × 0.52 (mm3).
Statistical analysis
All statistical analysis was performed using the GraphPad Prism Software, Version 8 (GraphPad Software, San Diego, CA, USA). Significant differences were analyzed using two-tailed Student’s t-test or the one-way ANOVA. The value of P < 0.05 was considered statistically significant.