Samples
Fresh samples from lung cancer and corresponding normal adjacent tissue were obtained from patients at Shengjing of China Medical University between January 2011 and November 2013 with informed consent. None of the patients in the study received any chemotherapy or radiation therapy before surgery. This study was conducted with the approval of the Ethics Committee at Shengjing Hospital of China Medical University. Written informed consent was obtained from all patients. Research carried out is in compliance with the Helsinki Declaration. Tumor samples were stored at -80 °C for RNA extraction (the percentage of tumor tissue was >90 %).
Cell culture, reagents and transfection
HBE135, H1299, H157, H1395, H460 and H3255 cell lines were obtained from American Type Culture Collection (Manassas, VA, USA). Cells were cultured in RPMI-1640 (Invitrogen, Carlsbad, CA, USA) containing 10 % fetal calf serum (Invitrogen, Carlsbad, CA, USA), 100 IU/ml penicillin (Sigma, St. Louis, MO, USA), and 100 μg/ml streptomycin (Sigma). Cells were grown on sterilized culture dishes and were passaged every 2 days with 0.25 % trypsin (Invitrogen, Carlsbad, CA, USA).
A mimic negative control, miR-663a mimic, an inhibitor negative control and a miR-663a inhibitor were purchased from RiboBio (Guangzhou, China). miRNA mimic is small, double-stranded RNA molecule, designed to mimic endogenous mature miRNA molecules when transfected into cells. miRNA inhibitor is small, single-stranded RNA with chemical modification that regulate gene expression by binding to and inhibiting a specific mature miRNA. MiR-663a mimic and inhibitor were transfected using Dharmafect1 Transfection Reagent (Dharmacon Lafayette, CO, USA). Briefly, complexes containing the mimic or inhibitor were prepared according to the manufacturer’s protocol and then cells were transfected with mimic negative control (100nM), miR-663a mimic (100nM), inhibitor control (200nM) or miR-663a inhibitor (200nM), respectively.
siGENOME SMARTpool siRNA for JunD and Non-targeting siRNA #1 were purchased from Dharmacon (100nM per well). The cells were transfected with siRNA using the DharmaFECT 1 (0.20 μL/well; Dharmacon Lafayette, CO, USA) according to the manufacturer’s protocol.
Quantitative real-time PCR
Total RNA was extracted from fresh tissues and cells using Trizol (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. Quantitative real-time PCR was performed using SYBR Green PCR master mix (Applied Biosystems, Foster City, CA, USA) on 7900HT Fast Real-Time PCR System (Applied Biosystems, Foster City, CA, USA). Primers for miR-663a (Bulge-LoopTM miRNA qRT-PCR Primer Set for has-miR-663a, RiboBio, Guangzhou, China) and U6 (U6 snRNA qRT-PCR Primer Set, RiboBio, Guangzhou, China) were used for PCR analysis in accordance with the manufacturer’s protocol. Other primers are as followers: cyclin D1 forward, 5′-GCTGGAGGTCTGCGAGGA-3′, cyclin D1 reverse, 5′-ACAGGAAGCGGTCCAGGTAGT-3, cyclin E forward, 5′-AGCCAGCCTTGGGACAATAAT-3′, cyclin E reverse, 5′-GAGCCTCTGGATGGTGCAAT-3′, p21 forward, 5′-CCTCATCCCGTGTTCTCCTTT-3′. p21 reverse, 5′-GTACCACCCAGCGGACAAGT-3′. CDK4 forward, 5′-CCGAAGTTCTTCTGCAGTCC-3′. CDK4 reverse, 5′-GTCGGCTTCAGAGTTTCCAC-3′. CDK6 forward, 5′-GTGACCAGCAGCGGACAAAT-3′. CDK6 reverse, 5′-CCACAGCGTGACGACCACT-3′. MMP2 forward, 5′-TGTGTTCTTTGCAGGGAATGAAT-3′. MMP2 reverse, 5′-TGTCTTCTTGTTTTTGCTCCAGTTA-3′. MMP9 forward, 5′-CCTCTGGAGGTTCGACGTGA-3′, MMP9 reverse, 5′-TAGGCTTTCTCTCGGTACTGGAA-3′, β-actin forward, 5′-ATAGCACAGCCTGGATAGCAACGTAC-3′, β-actin reverse, 5′-CACCTTCTACAATGAGCTGCGTGTG-3′. A dissociation step was performed to generate a melting curve to confirm the specificity of the amplification. Each PCR analysis was performed in triplicate. The relative levels of gene expression were represented as ΔCt = Ct gene –Ct reference, and the fold change of gene expression was calculated by the 2-ΔΔCt method.
Western blot analysis
Total proteins from cells were extracted in lysis buffer (Pierce, Rockford, IL, USA) and quantified using the Bradford method. 50 μg protein was separated by SDS-PAGE. Samples were transferred to polyvinylidene fluoride membranes (Millipore, Billerica, MA, USA) and incubated overnight at 4 °C with antibody against cyclin D1(1:1000, Cell Signaling Technology, Boston, MA, USA), cyclin E (1:1000, Cell Signaling Technology, Boston, MA, USA), p21(1:1000, Cell Signaling Technology, Boston, MA, USA), CDK4(1:1000, Cell Signaling Technology, Boston, MA, USA), CDK6 (1:1000, Cell Signaling Technology, Boston, MA, USA), MMP2(1:1000, Cell Signaling Technology, Boston, MA, USA), MMP9(1:1000, Cell Signaling Technology, Boston, MA, USA) and JunD (1:1000, Cell Signaling Technology, Boston, MA, USA) and GAPDH (1:1000; Santa Cruz, CA, USA). After incubation with peroxidase-coupled anti-mouse/rabbit IgG (1:1000, Cell Signaling Technology, Boston, MA, USA) at 37 °C for 2 h, bound proteins were visualized using ECL (Pierce, Rockford, IL, USA) and detected using a DNR BioImaging System (DNR, Jerusalem, Israel). Relative protein levels were quantified using ImageJ software.
Colony formation assay
For evaluation of colony formation, cells were transfected for 48 h before being seeded into 6-cm cell culture dishes (800 per dish) and incubated for 14 days. The plates were washed with PBS and the colonies were stained with the Giemsa dye. The number of colonies with more than 50 cells was manually counted under the microscope.
Cell cycle analysis by flow cytometry
Cells (500,000) were seeded into 6 cm tissue culture dishes and cultured overnight. Forty eight hours after transfection, cells were harvested, fixed in cold 70 % ethanol washed with phosphate-buffered saline (PBS) and stained with 5 mg/ml propidium iodide in PBS supplemented with RNase A (Roche, Indianapolis, IN) for 30 min at room temperature. The cells were analyzed by flow cytometer (Becton-Dickinson and Co., San Jose, CA, USA). One-parameter histogram was plotted according to the distribution of nuclear DNA content in each cell detected by flow cytometer. Cells in each individual phase of the cell cycle were determined based on their DNA ploidy profile.
Matrigel invasion assay
Cell invasion assay was performed using 24-well transwell chambers with pore size of 8 μm, and the inserts were coated with 20 μl Matrigel (1:3 dilution, BD Bioscience, San Jose, CA, USA). Sixty hours after transfection, cells were trypsinized, transferred to the upper matrigel chamber in 100 μl serum-free medium containing 3 × 105 cells, and incubated for 18 h. Medium supplemented with 10 % FBS was added to the lower chamber as the chemoattractant. Then, the non-invading cells on the upper membrane surface were removed with a cotton tip, and the cells that passed through the filter were fixed in 4 % paraformaldehyde and stained with hematoxylin. The experiments were performed in triplicate.
Luciferase reporter assay
Reporter gene transfection and luciferase activity assay were performed as follows: cells in confluent growth on a 24 well plate were co-transfected with the firefly luciferase reporter (0.2 μg) along with the Renilla luciferase reporter (0.02 μg), which was used for normalization, using Attractene reagent (Qiagen, Hilden, Germany) according to the protocols provided by the manufacturers. The reporter plasmids of AP-1 were purchased from Biotime Biotechnology, China. The pAP1-Luc contains SV40 early enhancer/promoter. The AP-1 response element was listed as follows: GGCCTAACTG GCCGGTACCG CTAGCTGACT AATGACTAAT GACTAATGAC; CCGGATTGAC CGGCCATGGC GATCGACTGA TTACTGATTA CTGATTACTG. The luciferase activity was measured in cellular extracts using a dual luciferase reported gene assay kit (Promega, San Luis Obispo, CA, USA). The relative activity of the reporter gene was calculated by dividing the signals from firefly luciferase reporter by the signals obtained from Renilla luciferase reporter.
Validation for interaction of miRNAs and Target Genes using Luciferase Reporter Assays
A pmiR-RB-REPORT™ vector (Ribobio Co., Guangzhou, China) was used for 3′ UTR-luciferase reporter assays to detect interactions of miR-663a with JunD (Gene ID: 3727). The TargetScan Human database 6.2 http://targetscan.org/was used to identify miRNA binding sites. The Wild-type miR-663a target site in JunD 3′-untranslated region was CCCCGCC. The mutant miR-663a target site was CGGGCGC. The miR-663a mimic, miR-663a inhibitor and their corresponding negative controls (Ribobio Co. Guangzhou, China) were transfected with pmiR-RB-REPORT™-target gene UTR. Reporter assays were conducted in triplicate. The cells were co-transfected with 100 nM mimic and 100 ng/mL reporter plasmid by attractene agent (Qiagen, Hilden, Germany) according to the manufacturer’s instructions
Statistical analysis
SPSS version 11.5 for Windows was used for all statistical analyses. Student’s t-test was used to compare densitometry data on focus numbers between control and treated cells. All p values are based on a two-sided statistical analysis and p < 0.05 was considered to indicate statistical significance.