Bioinformatics analysis
Online tool miRDB was used to predict the target genes of miR-885-5p. The upregulated DEGs were screened out using GEPIA, with log2|FC|>2 and adjusted P<0.01. Venny 2.1.0 was then leveraged to overlap the common genes from miRDB and GEPIA. Finally, the common genes screened were subsequently uploaded to STRING (https://string-db.org) for protein-protein interactions analysis.
Sample acquisition and cell culture
Glioblastoma tissues and corresponding adjacent normal tissues were collected from 33 patients at the Fifth Affiliated Hospital of Zhengzhou University. The characteristics of 33 patients with glioblastoma are listed in Table 1. Our study was approved by the Ethics Committee of the Fifth Affiliated Hospital of Zhengzhou University. All cell lines were obtained from the BNCC (Beijing, China), such as glioblastoma cell lines (U251, U87, A172, SHG44 and SNB19) and the normal human astrocytes cell line (NHA). U251, U87, A172 and SNB19 cells were cultured in DMEM-H (Cat#: E600004, Sangon, China) with 10% fetal bovine serum and 100 U/mL streptomycin under 5% CO2 at 37 °C. The SHG44 cell line was cultured in RPMI-1640 (Cat#: E600028, Sangon, China) with the same culture conditions as other cell lines.
Cell transfection
The small interfering RNAs (siRNAs) of HOXA-AS2 (si-HOXA-AS2) and RBBP4 (si-RBBP4), miR-885-5p mimic, miR-885-5p inhibitor and negative control (NC) were synthesized and provided by GenePharma (Shanghai, China). Using Lipofectamine 2000 (Cat#: 11668019, Thermo Fisher Scientific, USA) at room temperature for 4 hours, the cells were transfected with 50 nM si-HOXA-AS2, si-RBBP4, miR-885-5p mimic and miR-885-5p inhibitor. After incubation for 2 days at 37°C, the transfected cells were collected to detect the transfection efficiency using qRT-PCR.
qRT-PCR
The total RNAs from 33 clinical tumor tissue samples, corresponding non-tumor tissue samples or cells, were separated using TRIzol Reagents (Cat#: 15596026, Thermo Fisher Scientific, USA). The isolated RNAs were subsequently reverse-transcribed into cDNA after detecting RNA concentration. The miRVana qRT-PCR miRNA Detection Kit (Cat#: AM1558, Thermo Fisher Scientific, USA) was utilized to reverse-transcribe miRNAs into cDNA according to the user’s manual. The SuperScript III First-Strand Synthesis SuperMix for qRT-PCR (Cat#: 11752050, Thermo Fisher Scientific, USA) was used to reverse-transcribe the lncRNAs and mRNAs into cDNA. After synthesizing cDNA, qRT-PCR was performed using the StepOnePlus Real-Time PCR System (Cat#: 4376600, Thermo Fisher Scientific, USA). The data of qRT-PCR were analyzed with the 2-ΔΔCt method. GAPDH was used as the internal control of mRNAs and lncRNAs, while U6 was utilized as the reference control of miRNAs. The sequences of the primers are illustrated in Table 2.
Subcellular fractionation location
The PARIS Kit (Cat#: AM1921, Thermo Fisher Scientific, USA) was used to separate nuclear and cytoplasmic RNAs. The isolated RNA products were analyzed using qRT-PCR. The GAPDH served as the cytoplasmic control, while U2 was used as nuclear control.
CCK-8 assay
The effect of the HOXA-AS2/miR-885-5p/RBBP4 axis on cell viability was assessed using the CCK-8 assay. Transfected U87 and U251 cells (100 μL) in the logarithmic growth phase were seeded into the 96-well plates at a density of 2000 cells/well before being incubated at 37 °C. After an incubation period of 0, 24, 48 and 72 hours, 10 μL CCK-8 solution was added to each well. The cells were later incubated for 2 hours according to the instruction manual of the CCK-8 Kit (Cat#: E606335, Sangon, China). The absorbance was measured at 450 nm with a microplate reader to assess cell viability.
BrdU assay
The BrdU Cell Proliferation ELISA Kit (colorimetric) (Cat#: ab126556) was purchased from Abcam (UK) for BrdU assay analysis. The transfected cells (1×105) were added to each 96-well plate. Then, 20 μL BrdU was added to each well and incubated for 24 hours. After incubation, the cells were fixed using a 200 μL/well fixing solution for 30 minutes. The cells removed from the fixing solution were later incubated with 100 μL/well anti-BrdU antibody for 1 hour at room temperature. Next, 100 μL/well Peroxidase Goat anti-mouse IgG was added to the cells and then incubated for 30 minutes at room temperature. Finally, the absorbance was measured at 450 nm to assess the ability of the cells to proliferate.
Cell adhesion assay
Type I collagen (10 μg/mL) or 10% bovine serum albumin was used to pre-coat 96-well plates overnight. Next, 5 × 103 cells/well transfected cells were added to the pre-coated 96-well plates and then incubated for 1 hour. After the incubation period, the non-adherent cells were removed, and the adherent cells were incubated with a recovery medium. Finally, 10 μL MTT was added to cells and incubated for another 2 hours. The absorbance was measured at 570 nm to evaluate cell adhesion.
Cell apoptosis detection
The cells transfected were resuspended in pre-chilled PBS and then diluted to 1 × 106 cells/ml using 1× Annexin binding buffer. Then, 5 µL of the Annexin V-FITC staining solution and 5 µL of 100 µg/ml PI staining solution was added to the cells and then incubated in the absence of light for 30 minutes. Finally, the apoptosis rate was detected using flow cytometry. This was done according to the manufacturer's instructions.
Nude mice xenografting assay
Female BALB/c nude mice 6-8 weeks of age (Beijing Vital River Laboratory Animal Technology Co., Ltd.) were intracranial injected with 3 × 104 U87 cells transfected with HOXA-AS2 knockdown recombinant lentivirus (Si-LNC) or the negative control (NC). The injection was carried out according to the methodology used in previous studies [25]. The growth of tumors in vivo was monitored by biophotonic imaging using a Xenogen IVIS 200 system (Xenogen, Palo Alto, CA). Images were captured and quantified with Xenogen Living Image 4.1 software. The image intensities were expressed as photon flux per second per square centimeter and steradian. After the nude mice were killed on day 29, the tumors were resected and subjected to HE pathology analysis.
Dual-luciferase assay
The segments of wild-type HOXA-AS2 and RBBP4 3’UTR containing the binding site of miR-885-5p and the segments of mutant HOXA-AS2 and RBBP4 3’UTR without the binding site of miR-885-5p were inserted into pmirGLO vectors. The corresponding recombinant vectors included pmirGLO-WT-HOXA-AS2, pmirGLO-MUT-HOXA-AS2, pmirGLO-WT-RBBP4, and pmirGLO-WT-RBBP4. These recombinant vectors were then co-transfected with miR-885-5p mimic or NC into U87 and U251 cells. After a transfection period of 48 hours, the luciferase activity was assessed with a dual-luciferase reporter assay system (Promega, USA).
RNA immunoprecipitation (RIP) assay
The interaction between HOXA-AS2 and miR-885-5p was further identified using RIP assay. The U87 and U251 cells transfected with miR-885-5p mimic were then cultured for 48 hours. Next, the transfected cells were collected using trypsin and then lysed with RNA lysis buffer. After the cells were lysed, the cell lysates were incubated with magnetic beads conjugated to anti-Argonaute2 (AGO2) or IgG1 as a negative control. After washing the unbound material on the magnetic beads with RIP buffer and PBS, the magnetic beads were resuspended with TRIzol Reagents (1 ml) to purify the bound RNAs. The extracted RNAs were eventually analyzed by qRT-PCR.
RNA pull-down assay
The interaction between RBBP4 and miR-885-5p was identified using an RNA pull-down assay. The cells (6×105/well) were seeded in 6-well plates and incubated overnight. Then, the biotinylated negative control (Bio-NC) and biotinylated miR-885-5p mimic (Bio-miR-885-5p) bought from RiboBio (China) were transfected with the cells using lipofectamine 2000. After 48 hours, the cells were incubated with streptavidin beads for 3 hours. Finally, qRT-PCR analysis was performed to measure RBBP4 expression.
Western blot assay
The total proteins were extracted using a RIPA lysis system (Cat#: C500005, Sangon, China). Next, the proteins were separated with 10% SDS-PAGE gel and then transferred to PVDF membranes (Cat#: F019532, Sangon, China). After blocking the membranes in 5% skim milk, the hybridization membrane was incubated at 4 °C overnight with primary antibodies RBBP4 (Cat#: D154089, Sangon, China), Twist (Cat#: ab49254, Abcam, UK), Slug (Cat#: ab51772, Abcam, UK), Vimentin (Cat#: ab92547, Abcam, UK), MMP-2 (Cat#: ab92536, Abcam, UK) and GADPH (Cat#: D190090, Sangon, China). The membranes were then incubated with the corresponding secondary antibody for 2 hours. Subsequently, the protein was detected using the ECL chemiluminescence kit (Cat#: C510043, Sangon, China) according to the manufacturer’s instructions.
Statistical analysis
The data were represented in the form of mean ± standard deviation (SD), and three independent data were collected for each experiment. The Student's t-test was used to statistically analyze two groups, while the one-way analysis of variance (ANOVA) test was used to statistically evaluate multiple groups. P< 0.05 was considered to be statistically significant.