Clinical tissue samples and immunofluorescence histochemical staining (IHC) staining
Human tissue chip (Cat No. HNasN132Su01) containing 107 of NPC tissues and 30 of para-carcinoma normal tissues was purchased from Shanghai Outdo Biotech Company (Shanghai, China) and was used to detect the expression of RPS15A. The detailed pathological characters and the informed consents from patients were collected. This study was approved by the Ethics Committee of Kunming Medical University. For the IHC staining of RPS15A, briefly, all the fixed tissues were firstly dewaxed followed by rehydrating. Then the tissues were incubated with primary antibody anti-RPS15A (1:100, Lot No.PA5-51314, Invitrogen) at 4°C overnight following antigen repair and blocking. The secondary HRP-conjugated goat anti-rabbit IgG (1:400, Lot No. ab97080, Abcam) were then incubated with tissue slides at 37°C for 1 h. These slides were finally colored by diaminobenzene (DAB), counterstained by hematoxylin, dehydrated by alcohol, transparent with xylene, and sealed by neutral gum, respectively. The results of IHC staining were reviewed by two independent histopathologists and scored by percentages of positive staining cells (1, 0~24%; 2, 25~49%; 3, 50~74%; 4, 75~100%) and the staining intensity (0, no staining signals; 1, light yellow; 2, pale brown; 3, seal brown). The final IHC scores were determined as product of percentages of positive staining cells and the staining intensity: 0 score (-), 1-4 scores (+), 5-8 scores (++), 9-12 scores (+++) [23].
Cell culture
The human NPC cell lines (CNE-2Z, C666-1, 5-8F, HONE-1) were purchased from the American Type Culture Collection (ATCC) (Manassas, USA). These cell lines were all cultured in 90% RPMI-1640 medium (Gibco, USA) supplemented with 10% fetal bovine serum (FBS) (Gibco, USA) and 1% Penicillin/Streptomycin (100 U/mL) (Beyotime, China). Cells were maintained in a 5% CO2 incubator at 37°C.
RNA interference and cell transfection
The RPS15A silencing lentiviral vector (shRPS15A) and its control vector (shCtrl) were constructed in Shanghai YiBR Bioscires Co., Ltd (Shanghai, China). According to the manufacturer’s instructions, three RNA interference sequences were firstly determined as follows: shRPS15A-1, 5’-GTGCAACTCAAAGACCTGGAA-3’; shRPS15A-2, 5’-GCGCATGAATGTCCTGGCAGA-3’; shRPS15A-3, 5’-GATGACCACAGAGCTGGGAAA-3’. Then these sequences were synthesized into double stranded DNA oligo followed by connecting it to BR-V108 plasmid (Yibeirui, China) to generate the shRPS15A lentiviral vectors. Subsequently, the connected products were transduced into Escherichia coli cells (Cat. #CB104-03, TIANGEN), and positive cloned plasmids were selected for further amplification. Then the validated plasmids were co-transfected with pMD2.G (Qiagen, China) and pSPAX2 (Qiagen, China) for lentivirus generation. For lentivirus transfection, the NPC cell lines were transfected with shRPS15A lentivirus or shCtrl lentivirus using Lipofectamine 2000 (Thermo, USA) at a multiplicity of infection (MOI) of 20. Transfection efficacy was determined by observing the GFP expression.
Real-time quantitative PCR (qPCR)
Total RNA was isolated from the NPC cell samples using TRIzol regent (Sigma, USA) according to its manufacturer’s protocol. The isolated RNA was quantified by Nanodrop 100 (Thermo, USA) and reversely transcribed into cDNA using Hiscript QRT supermix (Vazyme, China). The SYBR Green mastermixs Kit (Vazyme, China) and Biosystems 7500 Sequence Detection system were used to amplify targeted genes based on the cDNA template. The targeted genes expression was normalized by GAPDH and calculated according to the 2-ΔΔCt method. Specific primers used in this study were shown as follows: RPS15A-forward: 5’-CGCGCCGCCACAATG-3’ and reverse: 5’-CACAGTGAGAAACCGGACGA-3’; GAPDH-forward: 5’- TGACTTCAACAGCGACACCCA-3’ and reverse: 5’- CACCCTGTTGCTGTAGCCAAA-3’.
Western blotting (WB) analysis
Cell lysates were prepared by radioimmunoprecipitation (RIPA) lysis for total proteins extraction. The protein concentrations were quantified by bicinchoninic acid (BCA) Protein Assay Kit (HyClone-Pierce, USA). 20 μg of proteins were loaded and electrophoresed by 10% sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) (Invitrogen, USA) followed by transferring onto polyvinylidene difluoride (PVDF) membranes (Millipore, USA). The membranes were then blocked by 5% skimmed milk and then incubated with primary antibodies: anti-RPS15A (1:1000, Lot No. PA5-51314, Invitrogen), anti-AKT (1:1000, Lot No. 4685, CST), anti-p-AKT (1:500, Lot No. AF887-sp, R&D), anti-CCND1 (1:1000, Lot No. 2978, CST), anti-CDK6 (1:1000, Lot No. ab151247, Abcam), anti-PIK3CA (1:1000, Lot No. ab40776, Abcam) and anti-GAPDH (1:3000, Lot No. AP0063, Bioworld) at 4°C overnight. After TBST washing, the membranes were incubated with secondary horseradish peroxidase (HRP)-conjugated goat anti-rabbit (1:3000, Lot No. A0208, Beyotime) at room temperature for 1 h. Protein expression levels were visualized with enhanced chemiluminescence (ECL) kit (Millipore, USA). GAPDH served as an inner control.
Cell proliferation assay
Cell viability was assessed by MTT assays. In brief, the NPC cells were transfected with shCtrl or shRPS15A lentivirus until grew at 85% confluence. Cell were then harvested and plated into 96-well plates at a density of 2 × 103 cells per well. 24 h after inoculation, 20 μL of MTT solution (5 mg/mL) was added into each well 4 h before termination of culture and incubated for 4 h. After that, 100 μL of DMSO was added to stop reaction. Finally, the optical density (OD) value at 490 nm was determined by microplate reader (Thermo, USA) and the growth curve was plotted based on the OD value.
Colony formation assay
The NPC cell lines transfected with indicated lentivirus for 5 days were harvested for colony formation assays. The transfected cells were counted and seeded into 6-well plates at a density of 900 cells per well. After 8 days of culture, the cell colonies were fixed by 4% paraformaldehyde for 30 min and stained by GIEMSA for 5 min. Then the colony numbers were determined under microscope.
Cell apoptosis analysis
Cell apoptosis was examined by flow cytometry. Firstly, the NPC cell lines were transfected with indicated lentivirus and cultured until the cell fusion reached 85%. Cells were then collected and re-suspended for Annexin V-APC (eBioscience, USA) staining. 10 min of incubation away from light, cells were washed three times with PBS followed by quantification of positive staining cells by flow cytometer (Millipore, USA).
Cell migration analysis
Cell migration was evaluated by Wound-healing assays and Transwell assays. In brief, the NPC cell lines transfected with indicated lentivirus were harvested when grown at 80% confluence. For wound-healing assays, cells were then re-suspended, counted and plated into 96-well plates at a density of 5 × 104 cells per well. The next day, scratches were formed using a scratch tester to push from bottom center of the 96-well plate to top. After removing of exfoliated cells by serum-free medium washing, cells were then cultured with 0.5% FBS-containing medium until indicated time points. Cellomics (Thermo, USA) was used to determine migratory distance of cells in each group, and the migration rate was calculated based on the migratory distance.
For transwell assays, the required numbers of chambers were placed into an empty 24-well plate followed by addition of 100 μL cell suspensions. Besides, 600 μL of 30% FBS-containing medium was added into the lower chambers. After incubation for 24 h, the non-migrating cells were removed with cotton tip and then the cells were fixed with 4% paraformaldehyde for 30 min and stained with Giemsa for 5 min. The migratory cells were determined under fluorescence microscope (Olympus, Japan).
Mice xenograft Model
10 of BALB/c nude mice (female, four-weeks-old) were purchased from Beijing Vital River Laboratory Animal Technology Co., Ltd (Beijing, China). Animal procedures were approved by Animal Care Committee of Kunming Medical University (No. kmmu 20211172). The xenograft models were established by subcutaneous injection of C666-1 cells (4×106 per mice) transfected with indicated lentivirus. One week after injection, the tumor sizes were monitored twice weekly using a Vernier caliper, and the tumor volumes were calculated as follows: V=π/6×L×W2 (L, represents the longest diameter; W, represents the shorter diameter). At the end of this experiments, all mice were sacrificed by injection of pentobarbital sodium as described previously [24] and the tumor were removed for weighting, photographs and Ki-67 staining.
Human Apoptosis Antibody Array
The Human Apoptosis Antibody Array (Cat No. ab134001, Abcam) assay was performed to reveal the expression alterations of apoptotic proteins. Briefly, the C666-1 cell transfected with shCtrl or shRPS15A lentivirus were prepared and lysed by lysis buffer. Cell lysates were then blocked using blocking buffer followed by incubation with the biotin-conjugated anti-cytolines at 4°C overnight, and streptavidin-HRP at room temperature for 2 h, respectively. Finally, the pixel density on the membrane was evaluated by enhanced ECL and quantified by ImageJ software.
Bioinformatics analysis
The independent dataset GSE12452 containing 10 of normal nasopharyngeal tissue and 31 of NPC tissues were available on GEO database (https://www.ncbi.nlm.nih.gov). RNA-Seq data were expressed as Fragments Per Kilobase Million (FPKM). The differentially expressed genes (DEGs) between normal tissues and tumor tissues were determined by following criteria: |Fold Change| ≥ 1.5 and p value < 0.05. RPS15A was identified as a significant upregulated gene in NPC tissues compared to that in normal tissues.
Statistical analysis
Each experiment in this study was performed in triplicate. Graphpad Prism 8.04 software was used to perform statistical analyses and graph. Data were shown as mean ± SD. The two-tailed Student’s t-test was used to determine p values between two groups. For multiple groups, the p values were determined by one-way analysis of variance (ANOVA). A value of p<0.05 was considered statistically significant.