Bioinformatics analysis
miRDB was an online tool for prediction the target genes of miR-885-5p. The upregulated DEGs were screened out by GEPIA with log2|FC|>2 and adjusted P<0.01. Then, Venny 2.1.0 was performed to overlap the common genes from miRDB and GEPIA. Finally, the common genes screened out were uploaded to String (https://string-db.org) for protein-protein interactions analysis to identify the key gene.
Sample acquisition and cell culture
Glioblastoma tissues and corresponding adjacent normal tissues from 33 patients were collected from The Fifth Affiliated Hospital of Zhengzhou University. The characteristics of 32 patients with glioblastoma were list in Table 1. Our study was approved by the Ethics Committee of The Fifth Affiliated Hospital of Zhengzhou University. Glioblastoma cell lines including U251, U87, A172, SHG44 and SNB19 and normal human astrocytes cell line (NHA) were obtained from the BNCC (Beijing, China). 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. As for SHG44 cell line, it was cultured in RPMI-1640 (Cat#: E600028, Sangon, China) with 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). The cells were transfected with 50 nM si-HOXA-AS2, si-RBBP4, miR-885-5p mimic and miR-885-5p inhibitor using Lipofectamine 2000 (Cat#: 11668019, Thermo Fisher Scientific, USA) at room temperature for 4 hours. After incubation for 2 days at 37°C, the transfected cells were collected to detect the transfection efficiency by qRT-PCR.
qRT-PCR
The total RNA from 33 clinical tumor tissue samples and corresponding non-tumor tissue samples, or cells was separated using Trizol reagent (Cat#: 15596026, Thermo Fisher Scientific, USA) according to the instructions. Then, the isolated RNA was reverse transcribed into cDNA after detection of RNA concentration. miRVana qRT-PCR miRNA Detection Kit (Cat#: AM1558, Thermo Fisher Scientific, USA) was obtained to reverse transcribe miRNA into cDNA following the protocols. As for lncRNA and mRNA, the SuperScript III First-Strand Synthesis SuperMix for qRT-PCR (Cat#: 11752050, Thermo Fisher Scientific, USA) was used. After the synthesis of cDNA, the qRT-PCR was performed using StepOnePlus Real-Time PCR System (Cat#: 4376600, Thermo Fisher Scientific, USA). The data of qRT-PCR were analyzed with 2-ΔΔCt method. GAPDH was used as the internal control of mRNA and lncRNA, and U6 as the miRNA internal control. The sequences of primers were list in Table 2.
Subcellular fractionation location
PARIS Kit (Cat#: AM1921, Thermo Fisher Scientific, USA) was used to separated nuclear and cytoplasmic RNA. The isolated RNA products were analyzed by qRT-PCR. The GAPDH served as cytoplasmic control and U2 was used as nuclear control.
CCK-8 assay
The effect of HOXA-AS2/miR-885-5p/RBBP4 axis on cell viability was assessed by CCK-8 assay. Briefly, 100 μL transfected U87 and U251 cells in a logarithmic growth phase were seeded into 96-well plates at the density of 2000 cells/well for incubation at 37 °C. After incubation for an appropriate time ( 0, 24, 48 and 72 hours), 10 μL CCK-8 solution was added into each well to incubate cells in incubator for 2 hours based on the manual of CCK-8 kit (Cat#: E606335, Sangon, China). The absorbance was measured at 450 nm to assess the cell viability.
BrdU assay
BrdU Cell Proliferation ELISA Kit (colorimetric) (Cat#: ab126556) was purchased from Abcam (UK) for BrdU assay. Briefly, 1×105 transfected cells was added to each well of 96-well plates. Then, 20 μL BrdU was added to each well of 96-well plates for 24 hours incubation. After incubation, the cells were fixed using 200 μL/well fixing solution for 30 minutes. Removing the fixing solution, the cells were incubated with 100 μL/well anti-BrdU antibody for 1 hour incubation at room temperature. Next, 100 μL/well Peroxidase Goat anti-mouse IgG was added into the cells for 30 minutes incubation at room temperature. Finally, the absorbance was measured at 450 nm to assess the cell proliferation ability.
Cell adhesion assay
10 μg/mL type I collagen or 10% bovine serum albumin was used to pre-coat 96-well plates overnight. Next, 5 × 103 cells/well transfected cells were added into the pre-coated 96-well plates for 1 hours incubation. After incubation, the non-adherent cells were removed and the adherent cells were incubated with medium for recovery. Finally, 10 μL MTT was added to cells for additional 2 hours incubation, and the absorbance was measured at 570 nm for the assessment of cell adhesion.
The detection of cell apoptosis by flow cytometry
The cells after transfection were resuspended in pre-chilled PBS, and diluted to 1 × 106 cells/ml using 1× Annexin binding buffer. Then, 5 µL of Annexin V-FITC staining solution and 5 µL of 100 µg/ml PI staining solution were added to the cells for 30 minutes incubation in the dark. Finally, the apoptosis rate was detected by flow cytometry according to the flow cytometer manufacturer's instructions.
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 were pmirGLO-WT-HOXA-AS2, pmirGLO-MUT-HOXA-AS2, pmirGLO-WT-RBBP4 and pmirGLO-WT-RBBP4. Then, these recombinant vectors were co-transfected with miR-885-5p mimic or NC into U87 and U251 cells. After 48 hours transfection, the luciferase activity was assessed by dual-luciferase reporter assay system (Promega, USA).
RNA immunoprecipitation (RIP) assay
The interaction between HOXA-AS2 and miR-885-5p was further identified by RIP assay. Briefly, the U87 and U251 cells with transfection of miR-885-5p mimic were cultured for 48 hours. Then, the transfected cells were collected using trypsin, and lyzed using RNA lysis buffer. After the cells were lysed, 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 reagent (1 ml) according to the instructions to purify the bound RNA. The extracted RNAs was analyzed by qRT-PCR.
RNA pull-down assay
The interaction between RBBP4 and miR-885-5p was identified by RNA pull-down assay. Briefly, the 6×105/well cells were plated in 6-well plates for incubation overnight. Then, the biotinylated negative control (Bio-NC) and biotinylated miR-885-5p mimic (Bio-miR-885-5p) provided from RiboBio (China) were transfected the cells using lipofectamine 2000. After 48 hours, the cells were incubated with streptavidin beads for three hours. Finally, the qRT-PCR was applied to measure the DOCK1 expression that were pulled down by breads.
Western blot assay
Total proteins were extracted by RIPA lysis (Cat#: C500005, Sangon, China). Proteins were separated by 10% SDS-PAGE gel electrophoresis and transferred to PVDF membranes (Cat#: F019532, Sangon, China). After blocking the membranes in 5% skim milk, the hybridization membrane was incubated with primary antibodies RBBP4 (Cat#: D154089, Sangon, China) and GADPH (Cat#: D190090, Sangon, China) at 4 °C overnight. The membranes were continued to incubate with the corresponding secondary antibody for 2 hours, and the protein was detected using ECL chemiluminescence kit (Cat#: C510043, Sangon, China) according to the reagent instructions.
Statistical analysis
The data were represented as means ± standard deviations from three independent experimental analyses. Student's t-test was used for statistical analysis between two groups, while One-factor analysis of variance (ANOVA) test was used for statistical analysis among multiple groups. P< 0.05 was considered to be statistically significant.