Patient-derived samples
The research was approved by the Ethics Committee of the Ethics Committee of the Institute of Gastrointestinal Oncology, School of Medcine, Xiamen University. 37 paired infiltrative GC tissue samples and neighboring non-tumor tissues were collected from the Ethics Committee of the Institute of Gastrointestinal Oncology, School of Medcine, Xiamen University. The clinical features of infiltrative GC patients were exhibited in Table 1. None of the participating patients received other treatments before surgery. All participants signed written informed consents before starting this study.
Cell culture and transfection
Infiltrative GC cells XGC-1 (Patent No.: CN103396994A) was obtained from the Institute of Gastrointestinal Oncology, School of Medcine, Xiamen University (Xiamen, China). Human gastric epithelial mucosa cells (GES-1) was purchased from BeNa Culture Collection (Suzhou, China). These two cell lines were grown in Roswell Park Memorial Institute (RPMI)-1640 medium (HyClone, Logan, UT, USA) containing fetal bovine serum (FBS, 10%, HyClone) and streptomycin/penicillin (1%, Solarbio, Beijing, China) in a moist atmosphere with 5% CO2 at 37˚C.
Small interference (si)-circVPS33B and negative control (si-NC), as well as short hairpin (sh)-circVPS33B and negative control (sh-NC), were purchased from GenePharma (Shanghai, China). For pcDNA-HNRNPK generation, the full-length sequence of HNRNPK was cloned into the empty pcDNA3.1 vector (pcDNA-NC) (Life Technologies, Grand Island, NY, USA). MiR-873-5p mimic (miR-873-5p), miR-873-5p inhibitor (anti-miR-873-5p), and their corresponding negative controls (miR-NC and anti-miR-NC) were purchased from RiboBio (Guangzhou, China). XGC-1 cells were transfected with vectors or oligonucleotides by Lipofectamine 3000 reagent (Invitrogen, Carlsbad, CA, USA). The stable circVPS33B knockdown cells were obtained by infecting with lentiviral particles and selecting with puromycin (Solarbio).
Quantitative real-time polymerase chain reaction (qRT-PCR)
RNAsimple Total RNA Kit from TIANGEN (Beijing, China) was utilized for total RNA separation (tissue samples and cells). The complementary DNA was synthesized with the M-MLV First Strand Kit (Life Technologies) or Bulge-Loop miR RT-qPCR Starter kit (RiboBio) and then used for qPCR with the SYBR Green (Solarbio). The primers were used as follows: circVPS33B (Forward: 5’-GTGGTGTTCTTGGGTGGTTGT-3’; Reverse: 5’-CCGCTCTAGCACCTTTCTCTC-3’), VPS33B (Forward: 5’-ATGAGCCCTTTGGATCGAATTG-3’; Reverse: 5’-ATGCGGGGTCTGACCAAGA-3’), HNRNPK (Forward: 5’-CAATGGTGAATTTGGTAAACGCC-3’; Reverse: 5’-GTAGTCTGTACGGAGAGCCTTA-3’), β-actin (Forward: 5’-GCACCACACCTTCTACAATG-3’; Reverse: 5’-TGCTTGCTGATCCACATCTG-3’), miR-873-5p (Forward: 5’-CGCATGGCAGTGGTTTTACCCTA-3’; Reverse: 5’-ATCCAGTGCAGGGTCCGAGG-3’), and U6 small nuclear RNA (U6) (Forward: 5’-CGCTTCGGCAGCACATATACTAAAATTGGAAC-3’; Reverse: 5’-GCTTCACGAATTTGCGTGTCATCCTTGC-3’). The levels of circVPS33B, VPS33B, HNRNPK, and miR-873-5p were evaluated by 2-ΔΔCt method, and β-actin or U6 was used as an internal.
Actinomycin D and RNase R treatment
The medium containing Actinomycin D (2 μg/mL, Sigma, St Louis, MO, USA) was utilized to inhibit RNA transcription of XGC-1 cells (0, 4, 8, 12, or 24 h). Total RNA of XGC-1 cells was incubated with 3 U/μg RNase R (Geneseed, Guangzhou, China) for total RNA digestion.
3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazoliumbromide (MTT) assay
XGC-1 cells (5×103 cells) were seeded into 96-well plates and grown for different time (24 h, 48 h, or 72 h). After discarding the supernatant, MTT solution (100 μL, 0.5 mg/mL, Sigma) was supplemented into each well. After incubation for 4 h, the purple precipitate was dissolved with dimethylsulfoxide (DMSO) (150 μL, Sigma). Next, the Microplate Reader (Bio-Rad, Hercules, CA, USA) was utilized to evaluate the absorbance at 570 nm.
Plate clone assay
XGC-1 cells (5×103 cells/well) were seeded onto 6-well plates. 2 weeks later, XGC-1 cells were fixed by paraformaldehyde (4%, Sigma) and stained with crystal violet (0.5%, Sigma). Next, an inverted microscope (Nikon, Tokyo, Japan) was utilized to count and photograph the colonies (> 50 cells/colony).
Wound healing and transwell assays
The migration of XGC-1 cells was analyzed by wound healing and transwell assays. For wound healing assay, a wound on the cell layer was created using a pipette tip (100 μL) when the transfected XGC-1 cells reached 90% confluence. The pictures of the cells at 0 h and 24 h were photographed with an inverted microscope (Nikon). The migration rate was calculated according to the following equation: cell migration rate (%) = (1-the distance following healing/the distance prior to healing) ×100%.
For transwell migration assay, the serum-free containing transfected XGC-1 cells (1×105 cells) was added to the top chamber of the transwell chamber (8 μm, Costar, Cambridge, MA, USA). The cell medium containing 10% FBS was supplemented into the bottom of the transwell chamber. After removing the cells on the upper surface of the membrane, the remaining cells were fixed and stained with paraformaldehyde (4%, Sigma) and crystal violet (0.5%, Sigma), respectively. The migrating cells were calculated with an inverted microscope (Nikon) at 100 × magnification.
For transwell invasion assay, its method was the same as the cell migration assay. It was worth noting that the transwell chamber of the invasion assay was pre-coated with Matrigel (Sigma).
Western blotting
Total protein (tissue samples and cells) was separated using the RIPA lysis buffer (Solarbio). All antibodies were purchased from Santa Cruz Biotechnology (Santa Cruz, CA, USA). Western blotting was executed in light of the previous research [27]. The immunoblot was visualized through the enhanced chemiluminescence reagent kit (Beyotime, Shanghai, China). The primary antibodies including: anti-β-actin (sc-8432), anti-ki-67 (sc-23900), anti-E-cadherin (sc-21791), anti-N-cadherin (sc-59987), anti-vimentin (sc-373717), and anti-HNRNPK (sc-28380). Also, m-IgGκ BP-HRP (sc-516102) was used as the secondary antibody.
Analysis of extracellular acidification rate (ECAR) and oxygen consumption rate (OCR)
The XF96 Extracellular Flux analyzer (Seahorse Bioscience, Chicopee, MA, USA) was utilized for the assessment of the ECAR and OCR of transfected XGC-1 cells. In short, the cells (1×104) were seeded into a Seahorse XF 96 cell culture microplate. The Seahorse XF Glycolysis Stress Test Kit (Seahorse Bioscience) was applied for ECAR analysis. In short, glucose, oligomycin, and 2-deoxy-D-glucose (2-DG) were sequentially injected into each well at the specified time point after baseline measurement. The Seahorse XF Cell Mito Stress Test Kit (Seahorse Bioscience) was utilized for OCR evaluation. In brief, oligomycin, p-trifluoromethoxy carbonyl cyanide phenylhydrazone (FCCP), and rotenone (Rote) plus antimycin A (AA) were sequentially injected into each well after baseline measurement. At last, the data were analyzed with the Seahorse XF-96 Wave software, and ECAR and OCR were presented in mpH/min and pmoles/min, respectively.
Glycolysis assay
The supernatant of transfected XGC-1 cells was collected. The amount of lactate and glucose in the supernatant was assessed with a Glucose Assay kit (Sigma) or Lactate Assay kit (BioVision, Mountain View, CA, USA) in light of the manufacturer’s instructions. Glucose uptake was analyzed by the difference between the glucose concentration and the control group.
Subcellular fractionation and localization
The nuclear RNA and cytoplasm RNA of XGC-1 cells were isolated by the PARIS kit (Life Technologies). Expression of circVPS33B in the nuclear and cytoplasm of XGC-1 cells was detected by qRT-PCR, and U6 and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) were used as controls for nuclear and cytoplasm, respectively. The primers for GAPDH were as follows: (Forward: 5’-GACTCCACTCACGGCAAATTCA-3’; Reverse: 5’-TCGCTCCTGGAAGATGGTGAT-3’)
Dual-luciferase reporter assay
The luciferase reporter assay kit (Promega, Madison, WI, USA) was employed to evaluate the luciferase activities of luciferase reporter vectors. The binding sites of circVPS33B in miR-873-5p were predicted with the circInteractome database. The binding sites between HNRNPK and miR-873-5p were predicted with the TarBase, TargetScan, miRDB, and miRWalk databases. The fragments of wild type (WT) circVPS33B (circVPS33B-WT), mutant (MUT) circVPS33B (circVPS33B-MUT), WT 3’UTR of HNRNPK (HNRNPK 3’UTR-WT), and MUT 3’UTR of HNRNPK (HNRNPK 3’UTR-MUT) containing miR-873-5p binding sites were synthesized and inserted into the psiCHECK-2 vectors (Promega), respectively, to construct the luciferase reporter vectors. After cotransfection of the luciferase reporter vectors with miR-873-5p or miR-NC into XGC-1 cells, the luciferase activities were evaluated by normalizing the firefly luminescence to Renilla luminescence.
RNA pull-down assay
The biotinylated (Bio)-miR-873-5p, Bio-miR-NC, and Bio-miR-873-5p-MUT probes were bought from Sigma. The probe-coated bead was established by incubating a probe with the M-280 Streptavidin magnetic bead (Invitrogen). The lysates of XGC-1 cells were incubated with probe-coated beads. The RNA complexes were isolated with TRIzol reagent (Solarbio). QRT-PCR was executed to analyze the enrichment level of circVPS33B in RNA complexes.
In vivo tumorigenesis assay
The protocols of xenograft assay were authorized by the Animal Ethics Committee of the Institute of Gastrointestinal Oncology, School of Medcine, Xiamen University. 10 BALB/c nude mice (4-week-old) were bought from Vital River Laboratory Animal Co., Ltd. (Beijing, China). For xenograft assay, XGC-1 cells (1×106) with sh-circVPS33B or sh-NC were subcutaneously injected into the right flank of BALB/c nude mice. Tumor volume was measured with calipers every 7 days from the second week after injection. Until day 35, the mice were killed by cervical dislocation under isoflurane (5%) to take tumor tissues. Tumors volume was counted in light of the following equation: Volume = (length ×width2)/2. The mice were randomly divided into 2 groups with five mice per group.
Statistical analysis
Correlation among circVPS33B, HNRNPK, and miR-873-5p in infiltrative GC tissues were evaluated with the Pearson’s correlation analysis. Differences were deemed significant if P < 0.05. One-way variance analysis (ANOVA) with Turkey’s post hoc test was utilized to assess the differences among 3 or more groups. Paired or unpaired Student’s t test was applied to compare the difference between 2 groups. Statistical analysis was implemented with GraphPad Prism 6 software (GraphPad, San Diego, CA, USA). Association between clinical features and circVPS33B expression of infiltrative GC patients was analyzed by Chi-square test. The experiments in vitro were repeated at least 3 times, and data were exhibited as the mean ± standard deviation.