Reagents
Antibodies against Flag (catalog number: M185-3L) and β-actin (M177-3) were purchased from Medical Biological Laboratories (Nagoya, Japan). Antibodies against matrix metalloproteinase (MMP)2 (A11144) and MMP9 (A0289) were obtained from ABclonal (Woburn, MA, USA). Antibodies against P21 (2947), cyclin D1 (2978), c-Jun N-terminal kinase (JNK; 9252), phosphorylated (p)-JNK (4668), protein kinase B (AKT; 4691), p-AKT (4060), p38 (9212), p-p38 (4511), extracellular signal-regulated kinase (ERK; 4695) and p-ERK (4370) were purchased from Cell Signaling Technology (Danvers, MA, USA).
The JNK inhibitor JNK-IN-8 (HY-13319, MCE,USA) was dissolved in dimethyl sulfoxide (DMSO) and diluted into a 0.5-μM working solution with complete culture medium, and the same amount of DMSO was set as the control.
Bioinformatics analysis
Bioinformatics analysis was undertaken in accordance with the work of Jiangqiao and collaborators [13]. ccRCC’s gene sequence tertiary count data samples and clinical information are obtained through TCGA data portal. DESeq2 within the R Project for Statistical Computing (Vienna, Austria) was used to standardize counting data and analyze differentially expressed genes between cancer samples and normal samples. Standardized data were used primarily to analyze the visual expression, stage, grade and survival correlation of USP44 in ccRCC and adjacent non-cancerous tissues. According to USP44 expression, clinical samples of ccRCC were divided into two groups for analyses.
Kaplan–Meier survival curves were used to show the differences in overall survival between patients with high expression of USP44 and cases with low expression of USP44. Simultaneously, we calculated the correlation between USP44 expression and the age, sex, tumor stage and tumor grade of the patient through T-text, and the obtained data were visualized through ggplot2 within the R Project for Statistical Computing.
Cells
The human ccRCC line 786-O (CRL-1932) was purchased from BeNa Culture Collection (Manassas, VA, USA). Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; C11995500BT; Billings, MT, USA) [14]. Caki-1 (a cell line of human ccRCC that metastasizes to the skin) was purchased from the Chinese Academy of Sciences Cell Bank (TCHu135; Beijing, China) and was cultured in McCoy’s 5A culture medium (L630; Basal Media, Saint Louis, MO, USA) [15]. Then, 10% fetal bovine serum (FBS; F05-001-B160216; One Biotechnology, Sarasota, FL, USA), penicillin (100 U/mL) and streptomycin (100 μg/mL) were added to DMEM and McCoy’s 5A. 786-O cells and Caki-1 cells were cultured in a humidified environment at 37℃ containing 5% carbon dioxide.
Lentivirus of overexpressed USP44, and construction and production of short hairpin (sh)RNA USP44 lentivirus
An overexpressed vector with a flag tag and shRNA vectors of the USP44 (homo) gene were designed and constructed according the method described by Jiangqiao and colleagues [13]. The gene registration number is NM_001347937.1. pHAGE-3xflag was used as the carrier. The primers were h-USP44-NF, AAACGATTCAGGTGGTCAGG, h-USP44-NR, and AGTGTACCCAGAACCCTCCT. The sequence of pLKO.1-h-USP44-shRNA1 was CGGATGATGAACTTGTGCAAT. The sequence of pLKO.1-h-USP44-shRNA2 was GCACAGGAGAAGGATACTAAT.
Cell counting kit (CCK)8 assay
Cell viability was examined using a CCK-8 kit following manufacturer (44786; Dojindo, Tokyo, Japan) protocols [13]. 786-O cells and Caki-1 cells were inoculated in 96-well plates (167008; Thermo Scientific, Waltham, MA, USA). After cells had adhered to the plate, they were cultured further for 0, 12, 24, 36, 48, and 60 h, respectively. CCK8 reagents (10 μL) were added and absorbance at 450 nm measured.
5-bromo-2'-deoxyuridine (BrdU) experiment
The BrdU experiment was undertaken according to manufacturer (11647229001; Roche, Basel, Switzerland) instructions [13]. 786-O cells and Caki-1 cells were inoculated in 96-well plates. After 24 h and 48 h, the BrdU experiment was carried out.
Wound-healing test
786-O cells and Caki-1 cells were inoculated into six-well plates (140675; Thermo Scientific) at 3×105 cells per well and incubated overnight. After that, the original culture medium was replaced with DMEM containing mitomycin (10 µg/mL). Then, cells were cultured for 12 h. Cells were wounded with a pipette tip and photographs taken immediately (0 h) as well as 6 h and 12 h after wounding. Then, the Cell Migration Index was calculated using the following formula:
Cell Migration Index = (wound width at 0 h – wound width at 6 h or 12 h) × 100/wound width at 0 h
Cell-migration assay
Healthy 786-O cells and Caki-1 cells were resuspended in DMEM or McCoy’s 5A. Then, they were plated at 3×104 cells/well (786-O) or 5×104 cells/well (Caki-1) in the upper compartment of a Transwell™ chamber (3421; Corning, Corning, NY, USA). Meanwhile, DMEM containing 600 μL of 2% FBS or 600 μL of 10% FBS was added to the lower chamber, respectively. Cells were cultured for 2 h or 3 h (786-O) or 10 h or 24 h (Caki-1) with phosphate-buffered saline. Then, 600 μL of 4% paraformaldehyde solution was used to fix cells for 15 min at room temperature, and 600 μL of 0.1% crystal violet (548-62-9; Xinkang ,Hubei) was used to stain cells for 2 h at 37℃. Images were acquired under a microscope. The number of positively stained cells reflected the cell-migration ability.
Western blotting
Proteins were extracted from 786-O cells and Caki-1 cells according to standard protocols. Meanwhile, protease inhibitors (04693132001; Roche) and phosphatase inhibitors (4906837001; Roche) were added. Protein concentrations were determined using a Bicinchoninic Acid Protein Assay kit (23225; Thermo Fisher Scientific). Briefly, we separated protein samples by sodium dodecyl sulfate-polyacrylamide gel electrophoresis on 12.5% gels, and then transferred them to nitrocellulose membranes. We blocked the nitrocellulose membranes using 5% nonfat dry milk in TBS-T buffer and incubated them overnight with primary antibody at 4°C. After rinsing the blots extensively with TBS-T buffer, incubation with secondary antibodies for 1 h was undertaken. We applied a ChemiDoc™ XRS+ gel-imaging system (Bio-Rad Laboratories, Hercules, CA, USA) to detect the target bands.
Reverse transcription-polymerase chain reaction (RT-PCR)
The total mRNA of 786-O and Caki-1 cell lines was extracted with TRIzol® Reagent (15596-026; Invitrogen, Carlsbad, CA, USA). Then, total RNA was reverse-transcribed into complementary (c)DNA using a Transcriptor First Strand cDNA Synthesis kit (04896866001; Roche) according to manufacturer instructions. SYBR® Green (04887352001; Roche) was used to quantify the PCR-amplification products. mRNA expression of target genes was normalized to that of β-actin expression. All the primer information is in Table 1.
Statistical analyses
Data are the mean ± standard error. We used SPSS v19.0 (IBM, Armonk, NY, USA) for statistical analyses. The Student’s t-test was used to analyze all data. P<0.05 was considered significant.