2.1 Bioinformatic tools
The data of GSE2712, GSE73209 and GSE11151 chip were obtained by using “Wilms’ tumour” as the key word in the database. The PDGFRβ gene expression in the database was analysed by the NCBI data. We used NCBI (https://www.ncbi.nlm.nih.gov/) in the database dataset GSE2712 PDGFRB for VEGFA and correlation analysis. The GGStatsplot package in the R 4.0.3 software was used to draw the correlation map. The ClusterProfiler package (version:3.18.0) in R was used to analyse the GO function of potential targets and to enrich the KEGG pathway. Potential protein-protein interactions (PPIs) were analysed using the STRING database (http://string-db.org/).
2.2 Cell culture and reagents
The human WT cell line G401 cells and human umbilical vein endothelial cells (HUVECs) were purchased from the Cell Bank of the Chinese Academy of Sciences (Shanghai, China). All cells were cultured in high-glucose Dulbecco's modified Eagle's medium (DMEM; Gibco, Gaithersburg, MD, USA) containing 10% foetal bovine serum (FBS; OriCell) and 1% penicillin-streptomycin solution (Beyotime). The cultures were placed in a humidified incubator at 37°C and 5%CO2.
PDGF‐BB (15ng/ml) was purchased from PEPROTECH. DASA‐58 (30mM) (S7928) and C3K (0.15μM) (S8616) were purchased from Selleck. LY-294002 (30μM) was bought from APExBIO. Lactate (10mM) (V900136) was purchased from Sigma-Aldrich. The working concentrations of all the reagents were selected according to the manufacturer's instructions.
2.3 siRNA transfection
Small interfering RNA (siRNA) targeting PDGFRβ (si‐PDGFRβ) was designed and synthesised by RIB BIO (Guangzhou, China). Negative control siRNA (NC) was used as the control. When the density of adherent cells reached 40% in a six-well plate, the indicated siRNA was transfected into the cells using CP Reagent. After culturing at 37°C in a humidified atmosphere containing 5% CO2 for 48 h, cells were used for subsequent assays.
The siRNA sequences are as follows:
si‐NC sense, 5′‐UUCUCCGAACGUGUCACGUTT‐3′,
antisense, 5′‐ACGUGACACGUUCGGAGAATT‐3′,
si‐PDGFRβ sense, 5′‐GUGAGAAGCAAGCCCUUAUTT‐3′,
antisense, 5′‐AUAAGGGCUUGCUUCUCACTT‐3′.
2.4 Preparation of conditioned culture medium for tumour cells
A total of 48 h after transfection with siRNA, G401 cells were cultured in fresh DMEM for another 24 h. The cell supernatant was collected, centrifuged at 14,000 rpm for 20 min, filtered with a 0.22μm filter, and transferred to a refrigerated tube, which was stored at -20℃ and -80℃ for a short and long time, respectively.
2.5 Western blotting
A total of 48 h after transfection, each well was added to each DMEM medium. After 24 h of culture, the cell supernatant was collected as a tumour-conditioned medium, and the remaining cells were harvested using a cell scraper for total protein isolation. Western blotting was performed as previously described by Guo et al. [26]. The corresponding primary antibody catalogue numbers and dilutions were as follows: PDGFRβ (1:1000, ab32570, Abcam), p-PDGFRβ (1:1000, ab218534, Abcam), VEGFA (1:1000, ab52917, Abcam), and β-actin (1:100,000, AC026, ABclonal).
2.6 Cell counting kit‑8 (CCK‑8) assay
HUVECs were seeded in 96-well plates at a density of 2000 cells/well, cultured overnight, and incubated in fresh medium containing different groups of tumour-conditioned medium for 24 h. A total of 10 μL Cell Counting Kit-8 reagent (Boster, Wuhan, China) was added to each well and the cells were cultured for 2 h. Optical density (OD) was measured at 450 nm using a microplate reader (Thermo Fisher Scientific, Waltham, MA, USA).
2.7 Enzyme-linked immunosorbent assay (ELISA)
The supernatant of the G401 cells was collected in a centrifuge tube and centrifuged at 14,000 rpm for 20 min to remove cell debris and impurities. The supernatant was sampled for ELISA to measure extracellular levels of VEGFA. An ELISA assay was performed according to the manufacturer’s instructions using a QuantiCyto® Human VEGF ELISA kit (NeoBioscience, EHC108.96, Shenzhen, China).
2.8 Migration and invasion assays
Migration and invasion assays were performed in 24-well transwell chambers with a pore size of 8 μm (Corning Life Sciences, New York, USA), whereas invasion assays were performed by coating the upper chamber with Matrigel in advance (BD Biosciences). Ten thousand HUVECs were added to each well in the upper chamber, and 800 μl of tumour-conditioned medium from different groups was added to the lower chamber. After 24 h of co-culture, the upper chamber was removed, fixed with paraformaldehyde for 30 min, and stained with crystal violet for 20 min. The remaining dye in the chamber was carefully wiped with a cotton swab. After air drying the chamber, images were obtained using a microscope (Leica 200 ).
2.9 Matrigel tube formation assay
For the tube formation assay, 50 μl of Matrigel (BD Biosciences, San Jose, CA, USA) was added to each well of a 96-well plate. After polymerisation at 37°C for 30 min, HUVECs were cultured in tumour conditioned medium from different groups, with 25,000 cells/well. After incubation for 5 h in a humidified incubator at 37°C with 5% CO2, tubules were visualised under an inverted microscope (Leica 100 ) and analysed using ImageJ.
2.10 Wound healing assay
HUVECs were cultured in a six-well plate, and they reached at least 90% confluency. A sterilized 200 μL pipette tip was used to create a wound. The wells were then washed twice with PBS to eliminate cell debris and replenished with the tumour-conditioned medium of different groups. Images were obtained with a microscope(Leica)at 200 magnification for 0 and 24 h and analysed using ImageJ.
2.11 Statistical analysis
All experiments were performed in triplicates, and the data were analyzed with the SPSS 25.0 IBM (SPSS Inc., Chicago, IL, USA) and GraphPad Prism 9.0 (GraphPad Inc., La Jolla, CA, USA). The data are presented as the mean ± SD and were evaluated using one-way analysis of variance (ANOVA) or Student's t-test. Statistical significance was set at P < 0.05.