Tissue culture and establishment of stable cell lines
A549, H1299 and HeLa cells were obtained from the cell bank at Peking Union Medical University and were detected for STR profiles in china. Cells were grown in Dulbecco’s modified Eagle’s medium (DMEM, HyClone) supplemented with 10% fetal bovine serum (HyClone) and 100 units/ml penicillin and streptomycin in a humidified incubator with 5% CO2 at 37 °C. The RNA interference target sequences corresponding to TCAB1 (shRNA: TATCTGGGACGCATTCACT) and a scrable sequence (TTCTCCGAACGTGTCACGT) were subcloned into lentiviral vectors of GV152 backbone (vector containing a puromycin resistance gene; Genechem). The lentiviral of LV-TCAB1 were provided by Hesheng genomic technology. The cells were infected with the produced lentivirus in the presence of polybrene (8 μg/ml; Sigma) for 48 h, and then selected by 2 μg/ml puromycin (Sigma) for 7 days. The expression levels of the targeted gene were determined by RT-PCR and western blotting for knockdown efficiencies.
RNA extraction and qRT-PCR
Total RNA was isolated from HeLa stable cells using the RNeasy mini kit (Qiagen) following to the manufacturer’s standard protocol. The RNA concentrations and purity were determined using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific). A total of 1μg of RNA each was subjected to reactions to obtain cDNAs using a Reverse Transcription Kit (Promega). Quantitative Real-Time-PCR was performed by an ABI 7500 Real-Time PCR System (Applied Biosystems) using Maxima SYBR Green/ROX qPCR Master Mix (MBI Fermentas ). Thermal cycling conditions were 95°C for 30s, followed by 5s at 95°C and 1min at 60°C for 40 cycles. PCR amplification was performed using specific primers: p21 (CGAGACACCACTGGAGGGT; R: GAGGCACAAGGGTACAAGACA ); TCAB1 F: (F: TCAAGAAGGTGGTGAAGCA; R: GTCAAAGGTGGAGGAGTGG );and GAPDH(F: CAAGGCTGTGGGCAAGGT; R: CCTGCTTCACCACCTTCTT ). Relative quantities of mRNA were calculated using the comparative Ct method for each sample. Analyses were done in triplicate to confirm the data.
Western blotting
The cell culture samples were lysed in modified Radioimmune Precipitation Assay (RIPA) Buffer (Applygen) containing a protease inhibitor cocktail (Roche). The protein concentrations were measured using the BCA assay kit (Thermo Fisher Scientific). A total protein of 10-20 μg from each sample were loaded and subjected to 10% sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), and then transferred to PVDF filters (Millipore). Immunoprobing of target proteins were performed by incubating overnight at 4 °C with the primary antibodies against p21 (#10355-1-AP, Proteintech), TCAB1(#14761-1-AP, Proteintech) or ubiquitin (#D058-3, MBL). After rinses, HRP-conjugated secondary antibodies used for western blotting analysis were as follows: anti-rabbit IgG (#3012; Signalway Antibody) and mouse IgG (#3032; Signalway Antibody). The even loading of isolated proteins was verified with β-actin monoclonal antibody (#3700S, Cell Signaling Technology) or GAPDH monoclonal antibody (#10494-1-AP, Proteintech). The blotted filters were visualized for signals using enhanced chemiluminescence (ECL) reagents (GE Healthcare) according to the manufacturer’s instructions.
Staining of senescence-associated β-galactosidase
For SA-β-gal staining, cells were seeded into 12-well plates and cultured in a DMEM medium. After fixed for 20 min at room temperature in 4% paraformaldehyde, the cells were washed twice with 1× PBS. A freshly prepared SA-β-gal staining solution was used to incubated with the fixed cells overnight at 37 °C with the absence of CO2. Eight randomly selected representative fields were quantified for the percentage of SA-β-gal positive cells. Data were presented as mean ± SE.
Immunoprecipitatation and in vivo ubiquitination assay
To detect the levels p21 ubiquitination, A549-shTCAB1, H1299-shTCAB1 and shTCAB1 stable HeLa cells were pretreated with 20 μM MG132 (Merck Millipore) for 6 h. The whole cell lysates were collected from 10 cm dishes and incubated with anti-p21 antibodies overnight at 4 °C. Then, 20 μl beads conjugated with protein A/G were added and incubated for 1 h at room temperature. The beads were washed three times with the washing buffer (10 mM Tris·HCl, pH 8.0, 1 M NaCl, 1 mM EDTA, 1% Nonidet P-40) prior to immunoprecipitation. The released samples in 20 μl 2×SDS protein loading buffer were subjected to western blotting analyses using an antibody against ubiquitin.
Protein half-life determination
The transformed stable cells were treated with 100 μg/ml of cycloheximide for 0, 0.5, 1, 2, 3, 4 and 5 h. The whole cell lysates were prepared. The amount of 10 or 20 μg of total protein from each sample was analyzed by Western blotting with an anti-p21 antibody.
RNAi and transfection
To transiently silence p21, siRNA targeting p21 was synthesized (Hesheng genomic technology) and transfected with Lipofectamine™ RNAiMAX (Invitrogen) following the manufacturer’s instructions. The siRNA sequence target p21 was: CGUCAGAACCCAUGCGGCATT. Control insertion sequence was: UUCUCCGAACGUGUCACGUT.
3D terrain map
From TCGA database, the mRNA expression of TCAB1, p21 and p16 of a total of 514 lung cancer patients were retrieved. For better and fair comparison of genes of different expression levels and abundance, the expression levels of each gene were normalize by quartile ranking scales and classified into 9 group from low to high as “0 to 8”. Using the normalized levels as the x and y scales, TCAB1/p21 or TCAB1/p16 in our case, the averaged level of a third gene of interest (p53 in this study) could be ploted with the original raw values to generate a 3D terrain map. Both p53 wild-type (362) and p53 mutation (152) cases were analyzed and presented as comparative panels.