Databases used
The Chinese Glioma Genome Atlas (CGGA, http://www.cgga.org.cn/), the Cancer Genome Atlas (TCGA, http://cancergenome.nih.gov/), Rembrandt (http://www.betastasis.com/glioma/rembrandt/), and TargetScanHuman 5.2 (http://www.targetscan.org/vert_50/) databases were mined for relevant molecular data.
Cell lines and cultures
Human GBM cell lines (U251, T98, U87, and A172) were obtained from the Chinese Academy of Sciences Cell Bank (Shanghai, China). P3, the in vivo propagated primary GBM tumor cell line and the GFP-luciferase stable U251 (GFP+ U251) glioma cell line was kindly provided by Prof. Rolf Bjerkvig, University of Bergen. U251, T98, U87, and A172 Cells were grown in Dulbecco’s modified Eagle’s medium (DMEM; SH30022.01B, Gibco; Gaithersburg, MD, USA) supplemented with 10% fetal bovine serum (10082147 Hyclone; GE Healthcare Life Sciences; Pittsburgh, PA, USA), whereas P3 cells were grown in Neurobasal Medium (#21103-049, NBM; ThermoFisher Scientific; Waltham, MA,) supplemented with 2% B27 (#A3653401, ThermoFisher Scientific), 1% L-glutamine (#BE17-605E, BioNordika; Oslo, Norway), 1% penicillin/streptomycin (#17-603E, BioNordika) and 20 ng/mL EGF (#236-eg-200, R&D Systems; Minneapolis, MN) in 5% CO2 in a humidified incubator at 37°C.
SiRNA transfections and lentiviral transduction
Gene-specific siRNAs against NUSAP1 and TOP2A (GenePharma; Shanghai, China) were transfected into U251, T98 and P3 cells for 48 h using Lipofectamine 2000 (Invitrogen, 11668-027) according to the manufacturer’s instructions. Nonspecific random sequences were used as the non-specific negative control (Si-NC). Lentiviral vectors expressing human shRNA targeting NUSAP1 (shNUSAP1, LV2017-18615, GenePharma) or the scrambled-control (shNC) were used to generate stable cell clones expressing shNUSAP1 or a nonspecific shRNA as the control. Transfected clones were selected using 1 mg/mL of puromycin (Selleckchem). Western blot analysis was used to evaluate siRNA and shRNA knockdown efficiency. Sequences of the siRNAs used are the following: NUSAP1#1, 5’-GCA GGA UCA UUC AGA GAU ATT UAU CUC UGA AUG AUU CUG CTT-3’; NUSAP1#2, 5’-GCA CCA AGA AGC UGA GAA UTT AUU CUC AGC UUC UUG GUG CTT-3’; and NUSAP1#3, 5’-GGA AAU GGA GUC CAU UGA UTT AUC AAU GGA CUC CAU UUC CTT-3’; TOP2A#1, 5’-GAC UGU CUG UUG AAA GAA UTT AUU CUU UVA ACA GAC AGU CTT -3’; TOP2A #2, 5’- CUC CUA ACU UCU AGU AAC UTT AGU UAC UAG AAG UUA GGA GTT-3’; and TOP2A #3, 5’-GAU CCA CCA AAG AUG UCA ATT UUG ACA UCU UUG GUG GAU CTT-3’; and the non-targeting control, 5’- UUC UCC GAA CGU GUC ACG A-3’.
Cell proliferation and invasion assays
The EdU incorporation assay (C103103, Ribobio; Guangzhou, China) was used to determine cell proliferation according to the manufacturer’s protocol. Briefly, cells were seeded into 24-well plates at a density of 5.0 × 104 cells per well and incubated overnight. After treatment, EdU was incorporated into proliferating cells and detected through a catalyzed reaction with a fluorescently labeled azide. Five random views from images acquired with a fluorescence microscope were used to count EdU positive cells.
For invasion assays, inserts in transwell migration plates (8 μm pore size, Corning; Sigma-Aldrich; St. Louis, MO, USA) were coated with matrigel (Becton-Dickinson; Bedford, MA, USA) and incubated for 4 h at 37°C. Cells (2 x 104) in 100 μL DMEM without FBS were seeded into the upper chamber, and 600 μL of medium containing 10% FBS was added to the lower chamber. After 24 h at 37°C, cells remaining on top of the Matrigel in the upper chamber insert were removed with a cotton swab while cells that had migrated through the Matrigel to the lower side of the insert were fixed with 4% formalin for 15 min, rinsed twice with PBS, and stained with 0.1% crystal violet for 10 min. Five random views from images acquired under a light microscope were used to count migrated cells.
Immunohistochemistry and western blotting analysis
Immunohistochemical (IHC) staining of the target proteins and evaluations of the intensities of staining were performed as previously described24. Briefly, paraffin-embedded samples were sliced and mounted on microscopic slides. Heat-induced epitope retrieval was performed with a microwave in 10 mmol/L citric acid buffer at pH 7.2. The sections were blocked with goat serum, incubated with primary antibodies at 4°C overnight, rinsed with PBS and incubated with a horseradish peroxidase-linked goat anti-rabbit antibody. Results were visualized through the reaction with diaminobenzidine and sections were counter stained with Mayer’s hematoxylin. Western blot analysis of the target proteins in glioma cells and human glioma samples was performed as previously described25. β-actin and GAPDH were used as the loading controls. Primary antibodies used were the following: anti-NUSAP1 (#12024-1-AP, Proteintech; Chicago, IL, USA); anti-TOP2A (#MA5-32096; Invitrogen; Carlsbad, CA, USA); anti-MKI67 (#ab15580, Abcam; Cambridge, UK); mouse anti-β-actin (#TA-09, monoclonal, ZSGB-BIO; Beijing, China); and anti-GAPDH (#BA2913, BOSTER; Wuhan, China).
Flow cytometric analysis of apoptosis
GBM cells were seeded in 6-well plates and incubated for 72h. Floating cells were harvested, re-suspended in 1´ binding buffer, and incubated with Annexin V-FITC (BD Biosciences; San Jose, CA, USA) and propidium iodide according to the manufacturer's instructions. Apoptotic cells were detected with flow cytometry (ACEA Biosciences; San Diego, CA, USA), and the software Flowjo (Tree Star; Ashland, OR, USA) was used to analyze the data.
Intracranial xenograft model
The xenograft tumor model was generated and evaluated as previously described. Briefly, athymic mice (male; 4 weeks old; 20–30 g; Shanghai SLAC Laboratory Animal Co., Ltd; Shanghai, China) were randomly divided into four groups: U251-shNC (n = 6), U251-shNUSAP1 (n = 6), P3-shNC (n = 6) and P3-shNUSAP1 (n = 6). The mice were anesthetized with chloral hydrate and securely placed on a stereotactic frame. A longitudinal incision was made in the scalp and a 1 mm-diameter hole was drilled 2.5 mm lateral to the bregma. P3-shNC, P3-shNUSAP1, GFP-luciferase stable U251/ GFP+ U251-shNC or GFP-luciferase stable U251/GFP+ U251-shNUSAP1 glioma cells (2×105) in 10 μL of PBS were implanted 2.5 mm into the right striatum using a Hamilton syringe. GFP-luciferase stable/GFP+ U251 injected mice were monitored with bioluminescence imaging every week. Mice were injected with 100 mg luciferin (Caliper/PerkinElmer; Waltham, MA, USA), anesthetized with isoflurane, and subsequently imaged with a cooled charge-coupled device camera (IVIS-200, Xenogen; Alameda, CA, USA). Bioluminescence values of tumors were quantitated using the Living Image 2.5 software package (Xenogen). Mice were euthanized when their weight dropped by more than 20% and perfused with 4% paraformaldehyde in PBS. Excised tumour tissues were formalin-fixed, paraffin-embedded, and sectioned. Sections were either stained with hematoxylin and eosin (H&E) or used for IHC.
Statistical analysis
Three independent experiments were performed, and all statistical analyses and experimental graphs were performed using GraphPad Prism 8 software (San Diego, CA, USA). X2-tests were used to compare categorical variables, and continuous variables were analyzed using ANOVA and the Student’s t-test. P-values determined from different comparisons are indicated as follows: *P < 0.05; ** P < 0.01; and *** P < 0.001. P-values<0.05 were considered statistically significant.