Bioinformatics
The analysis of bioinformatic data on the expression level of SSRP1 in human lung cancer and corresponding normal tissues and the relationship between SSRP1 gene expression and overall survival rate in patients with lung cancer were assessed through the UALCAN (http://ualcan.path.uab.edu/index.html) and GEPIA (http://gepia.cancer-pku.cn/index.html) browsers.
Cell culture and human tissue specimens
The human lung cancer cell lines A549, NCI-H446, H1299 and PC9, murine cells (LLC) and the normal human lung epithelial cell B2B were obtained from the Department of Respiratory Medicine, First Hospital of Jilin University (Changchun, Jilin, China) and Basic Medical School of Jilin University (Changchun, Jilin, China). Cells were cultured in Dulbecco's modified Eagle's medium (DMEM; Gibco; Thermo Fisher Scientific, Inc., Waltham, MA, USA) containing 5.5 mmol/l D-glucose and supplemented with 10% FBS (BI, Israel), 100 U/ml penicillin and 100 mg/ml streptomycin. The cells were cultured in a 37 °C incubator with 5% CO2. Five tissue samples from lung cancer patients (mean age, 58.2±6.85 years, ranging from 49 to 68; three female patients and two male patients) were collected at the First Hospital of Jilin University from September 2018 to May 2019. Patients receiving radiotherapy or chemotherapy were excluded from our study. Patients whose tissue samples were used in this research had provided written informed consent under an IRB-approved protocol. This study was approved by the local institutional review board of the First Hospital of Jilin University. The study methodologies conformed to the standards set by the Declaration of Helsinki.
Transient transfection
The siRNA was purchased from Genepharma (Suzhou, China). The sequences of siRNAs were as follows: siSSRP1-1, sense, 5¢-GCCAUGUCUACAAGUAUGATT-3¢ and antisense, 5¢-UCAUACUUGUAGACAUGGCTT-3¢; siSSRP1-2, sense, 5¢-CCCAGAAUGGUGUUGUCAAATT-3¢ and antisense, 5¢-UUUGACAACACAUUCUGGGTT-3¢; and negative control, sense, 5¢ CACGCAGAACGTGAACACC 3¢ and antisense, 5¢ GGCAGTAGATAACGTGAGGGA 3¢. NCI-H446 and H1299 cells were transfected with siRNA in 96-well plates or 6-well plates for 48–72 h. The Interferin transfection agent (Thermo Fisher Scientific, Inc., Waltham, MA, USA) was used according to the manufacturer’s protocol.
Cell viability, proliferation and colony formation assays
NCI-H446 and H1299 cells were plated on 96-well plates at a concentration of 1 × 104 cells/well to determine cell viability with a Cell Counting Kit-8 (CCK-8; MCE, New Jersey, USA) at 24, 48 and 72 h after transfection. The OD450 was measured with a FLUO star Omega reader (BMG LABTECH, Ortenberg, Germany). Cell growth was assessed by counting at 24, 48, and 72 h after transfection at a concentration of 5 × 104 cells/well in six-well plates. A total of 100 cells/well were cultured in six-well plates for colony formation assays. At 5–7 days after transfection, the colonies were fixed with 4% paraformaldehyde and then dyed with 0.2% crystal violet. Finally, colony formation was measured with an IX71 inverted fluorescence microscope (Olympus, Shinjuku, Tokyo, Japan).
Cell cycle analyses
Cells were collected with 0.25% trypsin and washed twice with cold PBS, then fixed with 70%–75% frozen ethanol at −20 °C for 1 h or fixed overnight at 4 °C. Subsequently, cells were washed once with cold PBS and then resuspended in 200–500 µl cold PBS. Then, 20 µl RNase A solution was added, and samples were incubated in a 37 °C water bath for 30 min. Finally, 400 µl PI stain solution (BestBio, Shanghai, China) was mixed gently and incubated for 30–60 at 4 °C in the dark. The results were detected with an Accuri C6 flow cytometer (Becton Dickinson, Franklin Lakes, New Jersey, USA).
Apoptosis analyses
NCI-H446 and H1299 cells were plated on six-well plates at a concentration of 1 × 105 cells/well. Transfection experiments were performed the following day. Cells were harvested after 48 h and washed twice with PBS. Cells were resuspended in 400 µl 1× buffer, then stained with 5 µl Annexin-V-FITC and 5 µl PI (50 μg/ml) with an Annexin V FITC Apop Dtec Kit (BD Biosciences, San Jose, CA, USA) in the dark for 15 min at room temperature, and detected with an Accuri C6 flow cytometer (Becton Dickinson, Franklin Lakes, New Jersey, USA).
Cell migration and invasion assays
Cell migration assays were conducted with Transwell chambers (Corning Costar, Cambridge, MA, USA) with an 8-mm pore size. The lower chamber was filled with DMEM containing 20% FBS, and the upper chamber contained cells resuspended in serum-free DMEM, at a concentration of 5 × 104 cells per well. After cultivation under 5% CO2 for 48 h at 37 °C, the bottom surfaces of the polycarbonate membranes in the upper chamber were wiped with cotton swabs to remove residual cells, and cells were counted visually under an IX71 inverted fluorescence microscope (Olympus, Shinjuku, Tokyo, Japan) after staining with 0.1% crystal violet dye. Matrigel (BD Biosciences, San Jose, CA, USA) was also used in the Transwell chambers before cells were cultured in the invasion assays. Cell migration and invasion were determined by counting five random fields under an optical microscope. The data are presented as mean ± standard deviation.
Western blot analyses
Cells and tissues were harvested and lysed in RIPA buffer for 30 min at 4–8 °C. Proteins were detected and quantified with a BCA protein assay kit (Thermo Fisher Scientific, Inc., MA, USA). Protein samples (30–50 μg) were separated with 12% SDS-PAGE and transferred to polyvinylidene fluoride membranes. Nonspecific binding was blocked with 5% low-fat milk with Tween-20 for 2 h at room temperature. Subsequently, the membranes were incubated overnight at 4 °C with the following primary antibodies: anti-SSRP1 (Proteintech, Chicago, IL, USA), anti-p21 (Proteintech, Chicago, IL, USA), anti-CyclinD1 (Proteintech, Chicago, IL, USA), anti-GSK3β (Proteintech, Chicago, IL, USA), anti-p-GSK3β (Ser9) (Proteintech, Chicago, IL, USA), anti-β-catenin (Proteintech, Chicago, IL, USA), anti-Lamin B1 (Proteintech, Chicago, IL, USA), anti-β-actin (Proteintech, Chicago, IL, USA) and anti-cleaved caspase3 (Cell Signaling Technology, Beverly, Massachusetts, USA). Lamin B1, encoded by the LMNB1 gene, is composed of a two-dimensional matrix of proteins located next to the inner nuclear membrane, which has been highly conserved during evolution. Therefore, Lamin B1 is often used as a nuclear protein internal control. The membranes were scanned for statistical analysis by enhanced chemiluminescence with a gel image processing system (Tanon, Shanghai, China).
Nuclear extraction
A nuclear and cytoplasmic protein extraction kit was purchased from Beyotime (Beyotime Biotechnology Inc., Nantong, China). Specific experimental steps were performed according to the manufacturer’s protocol.
Animal experiments
The study was approved by the Animal Research Ethics Committee of Jilin University. The siRNA used in vivo was synthesized by Genepharma (Suzhou, China) and dissolved in PBS buffer. The dose of siRNA in nude mice was 0.5 mg/kg.
Ten BALB/c male nude mice (18–22 g) were purchased from Beijing Vital River Laboratory Animal Technology and housed under a 12/12 h light/dark cycle in an air-conditioned room at 22 ± 2 °C, and were given free access to food and water. All animal experiments were performed in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals, with the approval of the Scientific Investigation Board of the College of Basic Medicine, Jilin University. Ten nude mice were randomly divided into two groups equally (five mice per group). A 100 µl subcutaneous injection containing 1 × 106 NCI-H446 cells was delivered into the upper right back in mice in each group. When the tumor size reached 3–5 mm, siSSRP1 or negative control (NC, used with isodose PBS) was inoculated into the xenograft tumor by multi-point injection every 3 days. Tumor volume was calculated with the following formula: V = (length) × (width)2/2. After 28 days, mice were killed by intraperitoneal administration of barbiturates (240 mg/kg) followed by cervical dislocation. Tumor tissue was removed and frozen at −80 °C for protein analysis or fixed in 4% paraformaldehyde for hematoxylin-eosin (H&E) staining and immunofluorescence staining.
H&E staining and Immunohistochemistry
Tissues were fixed in 4% paraformaldehyde solution for at least 4 h at room temperature, and this was followed by dehydration, dipping in wax, paraffin embedding and cutting into sections. The sections were then H&E stained. For immunohistochemistry, sections were incubated with serum or BSA for 30 min at room temperature, and then were incubated with diluted primary antibody for 2 h and then with secondary antibody. The samples were observed under a BX53 fluorescence microscope (Olympus, Shinjuku, Tokyo, Japan).
Online searches of miRNA-related databases
The miRNA-related databases used in this research were as follows: TargetScan (http://www.targetscan.org/), DIANA-microT (http://www.microrna.gr/microT), miRDB (http://www.mirdb.org/), miRWalk (http://www.ma.uni-heidelberg.de/apps/zmf/mirwalk/) and starBase (http://starbase.sysu.edu.cn/).
Luciferase reporter assays
After co-transfection of fluorescein reporter vector and miR-28-5p mimics into HCT15 cells for 48 h, detection of luciferase activity was performed with a Dual Luciferase Reporter Gene Assay Kit (Beyotime Biotechnology Inc., Nantong, China) according to the manufacturer’s instructions.
Statistical analyses
Data analysis was performed on at least three independent experimental groups, and the results are expressed as mean ± standard deviation. Statistical analyses were performed in SPSS version 17.0. Comparison of the two sets of data was performed with unpaired Student's t-test. One-way ANOVA was followed by Dunnett’s test to compare more than two sets. Differences were considered significant at *p < 0.05 and **p < 0.01, vs. the NC group.