Cell lines and cell culture
HK-2, 786-0, A-498, ACHN and Caki-1 cell lines were purchased from the American Type Culture Collection (ATCC, USA). All cells were maintained in Dulbecco’s modified Eagle’s medium (HyClone; GE Healthcare, Logan, UT, USA) supplemented with 10% fetal bovine serum (FBS; Gibco; Thermo Fisher Scientific, Inc., Waltham, MA, USA) and 1% penicillin-streptomycin solution. Cells were maintained at 37°C in an incubator containing 5% CO2.
Human ccRCC tissue samples
All samples were obtained from patients with ccRCC who underwent partial or radical nephrectomy from 2016 to 2018 at Union Hospital of Huazhong University of Science and Technology (Wuhan, China). The excised tissues were immediately frozen in liquid nitrogen for subsequent experiments. No patients who underwent surgery received any antitumor treatment before surgery. The samples were obtained with written informed consent from each patient. This study was approved by the Huazhong University of Science and Technology Committee.
Immunohistochemistry and immunofluorescence staining
Four-micrometer sections prepared from paraffin-embedded C4-2 tissues were used for immunohistochemical staining. The sections were sequentially deparaffinized, rehydrated, and incubated for antigen retrieval. Blocking was performed with fetal bovine serum after the sections were incubated with 3% H2O2 at room temperature for 15 min. Then, the sections were incubated with primary antibodies overnight at 4°C. Immunodetection was performed with an HRP-conjugated secondary antibody for 1 h. DAB was used to visualize the immune complexes. Finally, nuclei were counterstained with hematoxylin.
For immunofluorescent staining, cells were fixed in 4% paraformaldehyde, permeated with 0.5% Triton X-100, and blocked with 5% goat serum in PBS for 1 hour at 37°C, which was followed by incubation with primary antibodies. Finally, Alexa Fluor 488-conjugated Donkey Anti-Rabbit IgG (H+L) (Abclonal, AS035) was used as the secondary antibody to generate a visible signal. DAPI was used to stain nuclei.
RNA Extraction, cDNA Synthesis and qPCR
Total RNA was extracted from tissues with TRIzol reagent (Thermo, Massachusetts, USA) according to the instruction manual, and 1 μg of enriched tissue or cell RNA was used in reverse transcription. A NanoDrop 2000 spectrophotometer (NanoDrop Technologies, Wilmington, USA) was used to measure the purity and concentration of the RNA solution. The housekeeping gene glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was used as an internal control to standardize the variability in expression levels. SYBR Green mix (Thermo, Massachusetts, USA) was used for qPCR analysis. The specific gene primer sequences are as follows:
GAPDH: forward, 5'-CCAGAACATCATCCCTGCCT-3',
reverse, 5'-CCTGCTTCACCACCTTCTTG-3';
NUDT1: forward, 5'-GGCCAGATCGTGTTTGAGTT-3',
reverse, 5'-TGAAGCAGGAGTGGAAACCA-3';
and HIF2α: forward 5'-TCGGAGAGGAGGAAGGAGAA-3',
reverse, 5'-GAGGAGAGGAGCTTGTGTGT-3'.
Transfection assay
The following HIF2α-targeted short hairpin RNAs and NUDT1- targeted short hairpin RNAs were designed and synthesized by Genechem Co. Ltd (Shanghai, China). The constructed lentivirus was used to infect A498 or 786-0 cells according to the manufacturer’s protocol. The plasmids for overexpression of NUDT1, and negative controls were purchased from Genechem Co. Ltd (Shanghai, China).
Western blotting assays
For western blotting assays, the tissues and cells were lysed in RIPA protein lysis buffer (Beyotime Institute of Biotechnology, Haimen, China) containing protease inhibitor cocktail and PMSF. Subsequently, the protein concentrations were measured using a BCA kit (Beyotime Institute of Biotechnology) according to the manufacturer’s instructions. A total of 40 μg of protein was subjected to SDS-PAGE, which was then separated by gel electrophoresis and transferred to polyvinylidene fluoride (PVDF) membranes. Five percent non-fat dried skim milk was used to block the PVDF membranes for 1 hour at room temperature. Then, the membranes were incubated with primary antibodies overnight at 4°C. Subsequently, the membranes were washed and incubated in blocking buffer with secondary antibodies for 2 hours at room temperature. Finally, ChemiDoc-XRs+ (Bio-Rad Laboratories, Inc., Hercules, CA, USA) was used to visualize the proteins.
The antibodies used for western blotting were as follows: NUDT1 (Abclonal, A13330), HIF2α (Abclonal, A7553), GAPDH (Proteintech, 60004-1-Ig), SOD2 (Abclonal, A1340), HO-1 (Abclonal, A11919), and CAT (Abclonal, A5275).
Cell viability assays
For cell viability assays, A498 and 786-0 cells were transfected with sh-NC and sh-NUDT1, respectively. Then, the cells were seeded in 96-well plates at a density of 2x103/well. The proliferation rate of cells was determined using the CCK8 method according to the manufacturer’s instructions. Cell viability was assessed at 0, 24, 48, 72 and 96 hours after treatment.
Colony formation assays
A498 and 786-0 cells transfected with shNUDT1 or the control were plated in 6-well plates at 1000 cells per well. After two weeks, the cells were fixed with methanol and then were stained with 0.05% crystal violet to enable visualization of the viable colonies (> 50 cells/colonies). The colony forming ability was evaluated from the staining results.
Wound healing assays
Cells were seeded in 6-well plates. The cells were wound in a straight line by a 10 µl pipette tip through the monolayer when the cells reached 70-80% confluence. Subsequently, the cells were washed with PBS to remove impurities and then were maintained at 37°C. Images were captured at 0, 12, and 24 hours post wounding.
Transwell assays
For migration and invasion assays, cells were incubated in serum-free medium for 24 hours. Migration and invasion assays were performed using uncoated and Matrigel™-coated Transwell® inserts according to the manufacturer’s instructions. Cells were seeded in the top chamber of the insert and then were allowed to invade through the Matrigel. After incubation for 24 hours, cells invading the lower surface of the membrane insert were fixed with 100% methanol. Then, the cells were stained with 0.05% crystal violet, and 10 regions were randomly selected for counting.
Measurement of intracellular ROS levels
Cells were stained using a Cell Active Oxygen Detection Kit (Deep Red Fluorescence, Abcam) according to the manufacturer's instructions and then were photographed using a fluorescence microscope.
Cellular MDA measurement
The method for measuring cell malondialdehyde (MDA) was based on a malondialdehyde (MDA) assay kit (Nanjing Jiancheng Biotechnology Research Institute, Nanjing, China). Intracellular MDA expression was measured using a Multi-Mode Microplate Reader (SpectramMax M5) at 532 nm.
Chromatin immunoprecipitation assay and promoter analysis (ChIP)
Chromatin immunoprecipitation assay was conducted by SimpleChIP® Enzymatic Chromatin IP Kit (Agarose Beads) #9002 obtain from CST, which was performed according to the manufacturer’s manual. The plasmid with the truncated NUDT1 promoter region was constructed by Tianyi Huiyuan, China. Cell lysates were pretreated with normal rabbit IgG and protein A-agarose. An anti-NUDT1 antibody (2.0 µg) was added to the cell lysate, and they were incubated together at 4 °C overnight. IgG was used as the negative control. The specific primer sets used to amplify the target sequence within the human NUDT1 promoter were designed as follows:
Control Forward 5'- CACCATTGCTAAACCACCCA-3'
Reverse 5'- AGGCTGAGTGGGCATGGG-3'
Site 1 Forward 5'- TGGCCAACATGATGAAACCC-3'
Reverse 5'- GGGTTCAGGCGATTCTCCT-3'
Site 2 Forward 5'- TCTCGAACTCCTGACCTCTG-3'
Reverse 5'- CAGCCTGGATGATAGCAAAACA-3'
Site 3 Forward 5'- CCGGTCTCTATGTCCATCTTTC -3'
Reverse 5'- GAGGGGAAGACAGCGACTC -3'.
Luciferase assays
The 3' UTR of NUDT1 was constructed into RiboBio (RiboBio, Guangzhou, China), and promoter regions of NUDT1 were constructed by Tianyi Huiyuan, China. Cells were placed in 24-well plates, and complimentary DNA was transfected using Lipofectamine 2000 (Invitrogen) according to the manufacturer’s instructions. pRL-TK was used as an internal control. The luciferase activity was measured using a double luciferase detection reagent (Promega), and it was performed according to the instructions.
In vivo tumor implantation
A total of 2×106 cells were injected subcutaneously into 6-week-old male nude mice purchased from Vital River Laboratory Animal Technology Co., Ltd. To evaluate the metastatic potential of tumor cells, a nude mouse tail vein metastasis model was used. Tumor growth was measured with a digital caliper every 4 days for 7 weeks. Tumor weight was measured when mice were sacrificed on day 49 after cell implantation. Immunohistochemical staining was conducted using a standard procedure as previously described.
Bioinformatics analysis
Three independent oxidative stress pathway-related gene sets from the Oncomine database (https://www.oncomine.org) were used for screening. Gene set enrichment analysis (GSEA) was used to assess pathways of enrichment in the gene set. The mRNA levels of genes in normal kidney tissue and ccRCC tissue and relevant information (clinical stage, gender, age, survival time, etc.) of ccRCC patients were obtained from the database of TCGA-KIRC (http://www.cbioportal.org/public-porta).
Statistical analysis
Data for at least three independent experiments are expressed as the mean ± SEM. All statistical analyses were performed using t-tests or ANOVA with Excel 2016 (Microsoft) and SPSS Statistics 22.0 (IBM SPSS, Chicago, IL) software. Linear correlation analysis was used to determine the correlation between gene expression levels. Receiver operator characteristic (ROC) curve and area under the curve (AUC) were plotted to detect the best cut-off point and then obtained the highest overall accuracy rate, thereby clarifying different clinical classifications. Pearson correlation coefficient was used to assess the correlation between two factors. p<0.05 was considered statistically significant.