Population
28 pairs of PDAC fresh frozen tissues and adjacent nontumor tissues between December 2016 and July 2017 were generous given from Pancreas Biobank, The First Affiliated Hospital with Nanjing Medical University, which is a part of Jiangsu Biobank of Clinical Resource. None of the patients received radiotherapy, chemotherapy or targeted therapy before surgery. RNA samples from the tissues was extracted in department of Gastroenterology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China. The experiments utilizing human samples were approved by the Ethical Committee of Medical Research, the Affiliated Drum Tower Hospital of Nanjing University Medical School (2016-191-01).
Cell culture
The human pancreatic cancer cell lines (PANC-1, SW1990, COLO357 and CF-PAC1) and the human pancreatic ductal cell line (HPDE) were purchased from GeneChem (Shanghai, China). Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Gibco, Thermo Fisher Scientific, Waltham, MA, USA) was supplemented with 10% fetal bovine serum (FBS) (Gibco, Thermo Fisher Scientific, Waltham, MA,
USA) and 1% penicillin and streptomycin (Solarbio, Beijing, China), and they were maintained in a 37 ℃ incubator containing 5% CO2. The medium was replaced every 24-48 h according to the cell density. Cells were observed under an inverted microscope and were digested with 0.25% trypsin (Gibco, Thermo Fisher Scientific, Waltham, MA,USA) to enable passaging of the cells when they reached 80% confluence.
Quantitative real-time PCR (qRT-PCR)
Total RNA was isolated using TRIzol reagent. Then, the concentration of RNA was measured using aspectrophotometer (Titertek-Berthold Colibri). Complementary DNA(cDNA) was synthesized using a PrimeScript RT reagent kit(Takara Bio Inc., China), and qRT-PCR was performed using SYBR Premix Ex Taq (Takara Bio Inc.).The threshold cycle (CT) values for circRHOT1 and E2F3 were normalized against the CT value of GAPDH, which was an internal control, while miR-125a-3p was normalized against U6 snRNA, which was an internal control. The relative RNA expression values were calculated using the 2-ΔΔCt method.
Western blot analysis
Protein was extracted using a Total Protein Extraction kit (KeyGEN Biotech, Nanjing, China), and the protein concentration was quantified using a BCA Protein Assay kit (KeyGEN Biotech, Nanjing, China). Each sample containing an equivalent amount of protein (20 µg) was separated by 10% sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and transferred to polyvinylidene difluoride (PVDF) membranes. After blocking with 5% skim milk powder for one hour at room temperature, the PVDF membranes were incubated overnight at 4°C with a rabbit antibody against E2F3 (1:1000, Affinity, USA) and a rabbit monoclonal antibody against GAPDH (1:1000) (Beyotime Biotechnology, Beijing, China). Then, the membranes were washed 3 times with TBS-T buffer, which was followed by incubation with a goat anti-rabbit secondary antibody (1:1000, Beyotime Biotechnology, Beijing, China) for one hour at room temperature. Immunoreactive proteins were detected using an ECL Reagent (Affinity, USA) and an automatic chemiluminescence image analysis system (Tanon 5200).
Colony formation assay
Cell culture dishes (35 mm) were used, and each dish was covered with 2 ml of complete medium and 800 cells. After culturing for 14 days at 37 °C, the colonies were fixed with 4% formaldehyde for half an hour, stained with 0.1% crystal violet solution for half an hour, imaged and counted.
CCK-8 assay
CCK-8 assays were performed with an Enhanced Cell Counting Kit-8(Beyotime Biotechnology, Beijing, China). PANC-1 cells were seeded into 96-well plates, and after adherence overnight, we transfected the cells according to the experimental design. Then,10 µl of CCK-8 solution was added to each well. After 4 h of incubation at 37 °C with 5% CO2, the absorbance was measured at 450 nm by a microplate reader. We collected data once a day at the same time for four days.
5-Ethynyl-20-deoxyuridine (EdU) assay
A Cell-Light EdU DNA Cell Proliferation kit from Donghuan was used (Shanghai, China). PANC-1 cells were seeded into 24-well plates and then were transfected. When the cell density was close to 80%, the cells were incubated with serum-free DMEM supplemented with 10 μM EdU for an additional 2 h at 37 °C, and then they were fixed with 4% formaldehyde. After EdU and DNA staining for 30 minutes each, images were immediately captured. All images were obtained with an Olympus FSX100 microscope (Olympus, Tokyo, Japan). The ratio of EdU-stained cells to Hoechst-stained cells was used to evaluate cell proliferation.
RNA interference and stable transfection
Two small interfering RNAs (siRNAs) targeting the back-splice junction ofcircRHOT1 (si-circRHOT1-1 and si-circRHOT1-2) were designed and synthesized by Genechem (Shanghai, China). After determining that si-circRHOT1-1knockdown efficiency was better than that of si-circRHOT1-2, the sh-circRHOT1 knockdown sequence si-circRHOT1-1 was packaged into a GV248 lentiviral vector by Genechem (Shanghai, China). A miR-125a-3p mimic, an inhibitor and siRNAs targeting E2F3 (si-E2F3) were designed and constructed by GenPharma (Shanghai, China). The cells transfected with the sh-circRHOT1 lentivirus were cultured with 3 µl/ml puromycin for four days to generate a stably transfected cell line. Lipofectamine 3000 (Invitrogen, USA) was used for siRNA and plasmid transfection.
Dual-luciferase assay
Luciferase vectors with the 3’UTR of circRHOT1 or E2F3 and their mutant versions, containing the Renilla luciferase gene (hRluc) and firefly luciferase gene (hLuc), were obtained from Genechem(Shanghai, China). 293T cells were plated in 24-well plates and were cultured overnight. Then, luciferase vectors were cotransfected into cells with the miR-125a-3p mimic or a mimic NC and were incubated for 48h. Luciferase assays were then performed using a Dual-Luciferase Reporter Assay System kit (E2920, Promega, USA). Firefly luciferase activity was normalized to Renilla luciferase activity and was expressed as a percentage of the control.
Transwell assay
Transwell chambers with Matrigel (BD Biosciences, CA, USA) were used to detect cell invasion. The bottom chambers were added 500 µl of complete medium.PANC-1 cells were digested and suspended in serum-free medium, and 200 µl was loaded into the upper chambers (containing 6×10^4 cells).After incubation at 37 °C for 24 h, the cells on the bottom of the upper chambers were fixed with 4% formaldehyde for half an hour, and then stained with 0.1% crystal violet solution for half an hour; images were then collected from five different fields of each sample. The number of invasive cells was counted by ImageJ.
Flow cytometry
Cell apoptosis was assayed by using an Annexin V-APC/7-AAD apoptosis kit (MULTI, China). PANC-1 cells were collected and suspended in 1× binding buffer, and then V-PAC and 7-AAD were added. After incubating in the dark for 15 minutes, the percentage of apoptotic cells was detected by flow cytometry (BD FACSCalibur).
Cell cycle analysis was performed using a Cell Cycle Staining kit (MULTI, China). PANC-1 cells were collected and suspended in DNA staining solution with 1% permeabilization solution; they were stained in the dark for 30 minutes, and then they were detected by flow cytometry (BD FACSCalibur).
Statistical analysis
Comparison of data between groups are presented as the mean ± standard deviation. Student’s t-tests, Fisher's exact tests, and Mann-Whitney tests were performed by using SPSS (v.13.0.0; SPSS Inc., Chicago, IL, USA) to determine statistical significance. *P < 0.05 was considered statistically significant, and **P < 0.01 was considered highly statistically significant.