Flow cytometry analysis of the cell cycle. The MGC803 cell line, which was authenticated by short tandem repeat analysis, was used in the present study.
Cells were collected by centrifugation, washed three times with ice-cold PBS and centrifuged again (Eppendorf Mastercycler Nexus SX1; Eppendorf). The supernatant was discarded and the cells were resuspended in 0.5 ml PBS. Next, 3.5 ml 70% pre-cooled ethanol was added, and the solution was stored at 4˚C overnight up to 1 month until use. The ethanol-fixed cells were then centrifuged in a Mastercycler Nexus SX1 (Eppendorf). Next, the supernatant was discarded and the cells were washed three times with PBS to remove the residual ethanol. Next, the cells were resuspended in 1 ml PI/Triton X-100 staining solution containing 0.2 mg RNase A and stained at 37˚C for 15 min. Subsequently, the cell cycle was determined using flow cytometry.
RNA extraction. RNA was extracted using the RNA extraction kit RNeasy Mini Kit (Qiagen, Inc.) following the manufacturer’s instructions. The reagents used in the experiment were RNase-free. Briefly, cells were resuspended in 350 µl buffer RLT containing 1% β-mercaptoethanol. Next, 350 µl 70% absolute ethanol was added, mixed by pipetting, transferred to an adsorption column and centrifuged in a Mastercycler Nexus SX1 (Eppendorf) at 10,000 x g for 15 sec. Upon discarding the effluent, 350 µl buffer RW1 was added, followed by centrifugation in a Mastercycler Nexus SX1 (Eppendorf) at 10,000 x g for 15 sec. Upon discarding the supernatant, 10 µl DNase I was added to 70 µl buffer RDD. The sample was mixed evenly, added to the membrane of the adsorption column and incubated at room temperature for 15 min. Next, 350 µl buffer RW1 was added, followed by centrifugation in a Mastercycler Nexus SX1 (Eppendorf) at 10,000 x g for 20 sec. Next, the collection tube was replaced, and 500 µl buffer RPE was added, followed by centrifugation in a Mastercycler Nexus SX1 (Eppendorf) at 10,000 x g for 20 sec. Upon discarding the supernatant, 500 µl buffer RPE was added, followed by centrifugation in a Mastercycler Nexus SX1 (Eppendorf) at 10,000 x g for 2 min. Upon discarding the flow-through, the collection tube was replaced, and the sample was centrifuged in a Mastercycler Nexus SX1 (Eppendorf) at maximum speed for 2 min. Next, the adsorption column was placed in a 1.5-ml centrifuge tube (Eppendorf) tube, and ~ 30 µl RNase-free water was added, followed by incubation for 1 min and centrifugation in a Mastercycler Nexus SX1 (Eppendorf) at 8,000 rpm for 1 min to collect the RNA. Nanodrop 2000 (NanoDrop Technologies; Thermo Fisher Scientific, Inc.) was then used to measure the concentration and purity of RNA.
Reverse transcription of RNA into cDNA. M-MLV Reverse Transcriptase (Invitrogen; Thermo Fisher Scientific, Inc.) was used according to the manufacturer’s instructions. Briefly, the following components were mixed in a 200-µl PCR tube: 1 µl oligo (dT) (500 µg/ml), 1 µl dNTP (10 mM), 2 µg total RNA and RNase-free water up to a total volume of 12 µl. Next, the mixture was placed in the PCR instrument, where it was heated and denatured at 65˚C for 5 min, before being readily placed on ice to cool. Next, the following components were mixed in another PCR tube: 4 µl 5X first strand buffer, 2 µl DTT (0.1 M), 1 µl RNase inhibitor (20 U/µl) and 1 µl M-MLV. Subsequently, 8 µl was added to the mixture prepared in the other aforementioned PCR tube, and then placed in the PCR instrument, where the reaction was performed at 37˚C for 60 min followed by incubation at 70˚C for 15 min to inactivate M-MLV. The obtained cDNA was stored at -20˚C for long-term storage.
Fluorescence quantitative PCR (qPCR). The fluorescence qPCR system consisted of 10 µl SYBR Green Mix (Roche Diagnostics), 1 µl upstream primer (4 µM), 1 µl downstream primer (4 µM), 1 µl cDNA and ddH2O to a final volume of 20 µl. The reaction conditions were as follows: Pre-denaturation at 95˚C for 10 min, denaturation at 95˚C for 15 sec and annealing at 58˚C for 1 min for 40 cycles. Fluorescence detection was performed after annealing and extension. When the amplification reaction was completed, a melting curve reaction was performed to analyze the product specificity, which started at 55˚C, increased by 0.5˚C every 30 sec and ended at 95˚C for a total of 81 cycles. The 2− ΔΔCq method was used for analysis, and GAPDH was used as an internal reference. The relevant sequences are provided in Table SI.
Western blotting. Cells were collected, washed with PBS, mixed with an appropriate quantity of lysis buffer and lysed for 30 min on ice. After ultrasonication for 1 min, the sample was centrifuged in a Mastercycler Nexus SX1 (Eppendorf) at 12,000 rpm for 10 min at 4˚C. The supernatant was collected and the protein concentration was determined by using the BCA method. Next, an appropriate quantity of 5X SDS was added to the protein sample, which was then denatured by boiling in a metal bath at 95˚C for 5 min and immediately subjected to SDS-PAGE or stored at -80˚C until further use. After preparing the stacking and resolving gels, the protein sample was diluted to 5 µg/5 µl with 1X SDS for loading. Next, the sample was subjected to electrophoresis: A voltage of 80 V was used for concentration for 30 min, which was changed to 100 V for ~ 1 h when the sample entered the separation gel. Next, the samples were transferred to a membrane by applying 100 V in an ice water bath for 2 h. The membrane was then blocked by incubating with 5% skimmed milk powder in TBS-Tween 20 (TBST) at room temperature for 2 h. Next, the membrane was incubated with the primary antibody (diluted 1:1,000 in blocking solution) at room temperature for 2 h or at 4˚C overnight. Next, the membrane was washed three times with TBST for 15 min each at room temperature on a shaker. Next, the membrane was incubated with the secondary antibody (diluted 1:5,000 in blocking solution) for 1 h at room temperature, followed by three washes with TBST at room temperature for 15 min each on a shaker. To develop the protein bands, solutions A and B of a chemiluminescence kit were mixed at 1:1 ratio, and ~ 500 µl mixture was added to each X-ray film, which were then wrapped in plastic film in a dark room and placed in an X-ray film holder. After pressing for 10 sec-3 min, the X-ray films were developed, fixed, dried and stored. The relevant antibody information is shown in supplementary 1.
Immunofluorescence. In the culture plate, the slides with climbed cells were washed three times with PBS for 3 min each and then fixed with 4% paraformaldehyde for 15 min. Next, the slides were washed three times with PBS for 3 min each. Next, 0.5% Triton X-100 (diluted in PBS) was used at room temperature for 20 min to permeabilize the cells. Upon washing the slides with PBS three times for 3 min each, the PBS was removed with absorbent paper, and normal goat serum was then added to the slides for blocking at room temperature for 30 min. Next, absorbent paper was used to absorb the blocking solution without washing. Subsequently, diluted primary antibody was added to each slide, placed in a humid box and incubated overnight at 4˚C. Next, a fluorescently labeled secondary antibody was added as follows: PBS-Tween 20 (PBST) was used to wash the slides three times (3 min each time). The excess liquid on the slide was the removed with absorbent paper, and the aforementioned diluted fluorescent secondary antibody was added in a dropwise manner, followed by incubation in a humid box at 20–37˚C for 1 h. Next, the section was immersed in PBST three times (3 min each time), and the nucleus was subjected to counterstaining as follows: DAPI was added in a dropwise manner and incubated for 5 min in the dark. Next, the excess of DAPI was removed by washing with PBST four times (5 min each time), and the liquid on the slide was removed with absorbent paper. Subsequently, the slide was mounted with a mounting solution containing a fluorescence quencher, and images were observed and collected under a fluorescence microscope.
MTT assay to detect cell proliferation. To determine the proliferation ability of cells, MTT assay was performed as previously described (24). Cellular suspensions were prepared and transferred into a 96-well culture plate, and 10 µl MTT reagent (Beyotime Institute of Biotechnology) was added to each well. The samples were then incubated for 4 h, and colorimetric changes were determined at an absorbance of 570 nm by using a microplate reader. The absorbance of the samples was normalized to that of a blank control.
EdU staining to detect cell proliferation. EdU is a thymidine analogue, which can insert thymine into replicated DNA during cell proliferation. EdU can react with Apollo fluorescent dye to detect the replicated DNA, thereby detecting the proliferative activity of cells (12). In the present study, the cell proliferation activity was detected via the specific reaction of EdU with Apollo488, and the resulting green fluorescence was indicative of proliferation in EdU-positive cells.