Primary ccRCC patients and tissue samples
A total of 533 ccRCC patient cohort with ClinicalMatrix and RNA sequencing data (HiSeqV2) were obtained from TCGA data portal. Patients with available prognosis data were selected when analyzing the relationship between CDCA5 expression and ccRCC progression. Besides, 20 paired tumorous and normal pericarcinomatous tissues were conserved in liquid nitrogen, which are collected from different pathological grade (WHO/ISUP 2016 grading system) of ccRCC patients undergoing nephrectomy at the Renji Hospital of Shanghai Jiaotong University. RT-qPCR, Western blot and immunohistochemistry (IHC) staining experiments were successively performed with these tissues. All patients provided written consent, and this study was approved by the Ethics and Research Committees of Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
Western Blot Analysis
Tissues or tumor cells were lysed with 2% sodium dodecyl sulfate (SDS) and the protein concentration were then measured with BCA protein assay kit. Next, proteins were separated by SDS-PAGE gel and transferred to a nitrocellulose membrane. After blocking, the membrane was incubated with different primary antibodies and secondary antibody (with washing between steps). Finally, the target protein bands were visualized via chemiluminescence system. Primary antibodies CDCA5 (ab192237) and eEF1A1 (ab157455) were obtained from Abcam; β-actin (sc-69879) and GAPDH (sc-32233) were obtained from Santa Cruz. Secondary antibody Rabbit IgG (#7074) and Mouse IgG (#7076) were bought from Cell Signaling Technology.
Immunohistochemistry
Immunohistochemistry was performed on tissue samples according to the standard streptavidin-peroxidase method. Briefly, after fixing, embedding, deparaffinizing, rehydrating and blocking, specimens were incubated with the anti-CDCA5 primary antibody (1:100 dilution) at 4°C overnight. After washing and incubating with biotinylated secondary antibody, the results were finally recorded with a Nikon Eclipse Ti microscope.
Rna Extraction And Rt-pcr
Trizol reagent was used to isolate total RNA from tumor samples and cells, and RNA was converted into cDNA with the cDNA synthesis kit according to the manufacturer’s protocol. Gene mRNA expression level was measured by RT-PCR on an ABI ViiA™ 7 System (Thermo Fisher, Waltham, MA, USA). GAPDH was used as the relative control for analyzing gene expression fold change. Primers used in this study were as follows: for gene CDCA5, forward 5′- CCATCTCCTACTAAGCCTCTGC − 3′ and reverse 5′- GCCACGATCCTCTTTAAGACGAT − 3′; For gene GAPDH, forward 5′- TGACTTCAACAGCGACACCCA − 3′ and reverse 5′- CACCCTGTTGCTGTAGCCAAA − 3′.
Lentiviral Vectors Construction And Transfection
Lentiviral particles were constructed according to the conventional protocol. Briefly, CDCA5 shRNA sequences or scrambled shRNA sequence were integrated into the GV358 backbone plasmid, which was obtained from GENE (Shanghai Genechem Co.,Ltd.). Then, the shRNA plasmid, Helper1.0 plasmid and Helper2.0 plasmid were co-transfected 293T cells. Supernatant of treated 293T cells was collected and filtered at 48-72h after transfection. Besides, the plasmids using Ubi-3FLAG(sigma)-MCS-SV40-puromycin to construct overexpression EEF1A1 lentiviral vectors. Tumor cells were infected with lentiviral particles in the presence of 10 µg/mL Polybrene regent. After treating media with puromycin for 2 weeks, ccRCC cells were collected for subsequent experiments.
Cell Culture And Cell Survival Assay
RCC cell lines 786-O and ACHN were obtained from the ATCC (American Type Culture Collection). 786-O cells were cultured in 1640 media with 10% fetal bovine serum (FBS, Gibco, Australia), and ACHN cells were cultured in MEM media with 10% FBS. All cells were maintained at 37°C with 5% CO2. After treatment, cell survival was determined by MTT assay according to the standard protocol at different time points.
Flow Cytometric Analysis
Cell apoptosis analysis after CDCA5 knockdown was performed by using annexin V and propidium iodide double supravital stain. Briefly, after treatment, cells were collected, fixed, stained and analyzed by flow cytometry. Results were analyzed by using ModFit software according to the manufacturer’s instructions.
Cell Migration Analysis
To investigate the effect of CDCA5 on ccRCC metastasis, cell wound healing and cell transwell migration test were also performed. For cell wound healing assay, cells after treatment were plated in 6-well plates with over 90% confluence, and a sterile 100µL pipette tip was used to scrape across cells. At special time points, cells that migrated into the wounded area were measured by a microscope. For cell transwell migration assay, the special transwell plates were used according the conventional protocol. Briefly, appropriate number of cells were collected and added to the transwell plate, and cells were cultured for 24h. Then, cells were fixed, stained and dried, and five view fields cells number were counted for each samples with a microscope. The mean value was used as the migratory cell number.
Tumor Models
Animal study were approved by the Experimental Animal Ethics Committee of Shanghai Jiao Tong University (Shanghai, China). 4 to 6-week-old female nude mice (BALB/cnu/nu) were used for establishing the ccRCC tumor xenograft models. After infecting with lentiviral particles, around 5×106 ACHN cells were collected and subcutaneously injected into the flank region of mice. When the tumors reached approximately 200 mm3, tumor volumes (V = length×width2/2) and body weights were measured twice a week using a caliper and an iron-balance. At the end of experiments, all the mice were sacrificed and the tumors were harvested, photographed, weighed, and saved in liquid nitrogen.
Lc-ms/ms Analysis
Liquid chromatography–tandem mass spectrometry (LC-MS/MS) analysis was performed to screened out the potential interacting proteins of CDCA5. Firstly, ACHN cells were overexpressed with FLAG-CDCA5, and then cell lysates were collected in lysis buffer on ice. After centrifugation, the supernatants were incubated with an anti-Flag or anti-IgG antibody. Secondly, protein FLAG-beads were added to the supernatants, and proteins were eluted and subjected to SDS-PAGE electrophoresis. After protein digestion and peptide selection, LC-MS analysis was performed with the PD/MASCOT software. Finally, we conducted PPI (protein protein interaction) network analysis to select the potential interacting proteins. Besides, coimmunoprecipitation (Co-IP) experiments were performed to confirm our findings.
Statistical analysis
CDCA5 expression level in different groups were compared by using the student’s t test, and the Kaplan-Meier method with log-rank test was plotted to analyze the overall survival curves. All experiments were performed for over three times, and data were presented as mean ± SD. Significant differences between values obtained from different groups were determined using the two-tailed student’s t-test analysis. All statistical analyses were performed using Graphpad Prism 7.0, and P < 0.05 was considered statistically significant.