Cell proliferation assay
Cell viability was determined by the CCK8 assay kit (Dojindo). Briefly, the cells were seeded at a density of 5×103 cells per well of 96-well plate, in 200 μl DMEM medium (10% FBS). After incubation with different concentrations of neferine, 10 μl of CCK-8 reagent was added to each well and the absorbance was measured at 450 nm 2 h later. All experiments were repeated three times.
Clonogenic assay
For the clonogenic assay, single-cell suspensions were prepared and 500 cells were seeded in 6-well plates overnight. Cells were treated with various concentrations of Neferine for 2 weeks. Cell colonies were fixed with Methanol, and stained by 0.1% crystal violet, then photographed and scored. Colonies of more than 50 cells were counted to determine the surviving fraction. All experiments were repeated three times.
Cell cycle analysis
For the cell cycle analysis, single-cell suspensions were prepared and 3×104 cells were seeded in 6-well plates overnight. After treated with indicated concentrations of neferine for 24 h, the cells were washed three times with PBS, trypsinized and collected by centrifugation at 1000 rpm for 3 min. Then, cells were fixed in 3 ml of cold 75 % ethanol at −20 °C overnight. After centrifugation at 1000 rpm for 5 min, cells were washed by 2 ml cold PBS and centrifugated gain, cells were resuspended and incubated with 0.5 ml of PBS containing 100 μg/ml RNase (Beyotime) and 5 μg/ml propidium iodide (Yeasen) at room temperature for 30 min. Cell cycle distribution was analyzed by flow cytometry (BD Biosciences).
Annexin V apoptosis assay
Apoptotic cells were identified by FITC Annexin V Apoptosis Detection Kit (BD Bioscience). 3×104 cells were seeded in 6-well plates overnight. After treated with indicated concentrations of neferine for 48 h, the cells were washed three times with PBS, trypsinized and collected. Cells were resuspended in binding buffer and incubated at room temperature for 15 min in the dark after 5 μl FITC Annexin V and 10 μl PI were added. Apoptotic cells were analyzed by flow cytometry in 1 h.
ROS assay
Intracellular ROS levels were determined by the DCFH-DA fluorescent probe (Beyotime). 3×104 cells were seeded in 6-well plates overnight. After treated with indicated concentrations of neferine for 12h, the cells were incubated with DCFH-DA for 30 min and washed three times with PBS. Then DCF fluorescence was detected by flow cytometry (FITC-Channel). Fluorescence microscopy (Carl Zeiss) was used to photograph the cell.
Cell migration assay
The cell migration assay was performed using the Transwell system (24-wells, 8-μm pore size with polycarbonate membrane, Corning Costar). 5.0×105 Cells were suspended in serum-free medium and added to the upper chamber, 700μL of complete medium (10% FBS) was added to the lower chamber. After 4 h, the media in the upper chambers were replaced by media with various concentration of neferine. After 36 h, the chambers were fixed with paraformaldehyde, and stained by 0.1% crystal violet. The non-migrated cells were wiped off from upper surface of chamber using cotton swabs. The successfully migrated cells were last counted on 3 random fields.
Scratch assay
Scratch assays were applied to determine cell mobility affected by Neferine. 1×106 cells were seeded on a 6-well plate in the complete medium overnight to obtain a full confluent monolayer. After 12 h of starvation, a 20μL pipette tip was used to make a straight cell-free “scratch” on the well plate. The well was washed with PBS and added serum-free medium with different concentration of Neferine. Last, the migration of cells was photographed using a phase contrast microscope. Photographs were taken of cells at the matching reference points initially and then at 12 h intervals. The decreased square of the scratch were analyzed quantitatively.
Western blot analysis
Briefly, cells were collected after specific treatments and then lysed with RIPA. The concentration of protein was assayed using the Pierce BCA Protein Assay Kit (Thermo). 20μg of each sample was resolved into SDS-PAGE gels and then electro-transferred onto a PVDF membrane (Millipore). The membrane was blocked with 5% skimmed milk for 1h at room temperature and incubated overnight with primary antibody at 4℃. The membrane was washed and incubated with HRP conjugated secondary antibody for 1h. The protein bands were detected by a chemiluminescence system (Immobilion Western, Millipore). β-actin was used as an internal control.
The related antibodies:Anti-cleaved caspase 3 (CST and Santa); Anti-cleaved caspase 9, Anti-cleaved PARP1, anti-Beclin 1 and Anti-p62 (Proteintech); Anti-Bax (Beyotime) and Anti-Bcl2 (Santa); Anti-LC3-I/II (Abcam). The secondary mouse and goat antibodies (Beyotime).
Transmission Electron Microscopy (TEM) assay
After treated with neferine for 24 h, HN30 and CAL27 cells were fixed with glutaraldehyde and OSO4, dehydrated with graded ethanol, embedded in propylene oxide, sectioned at 70nm and stained with uranyl acetate nd lead citrate. The autophagosomes in cells are visualized with the electron microscope as described in previous method[19, 20].
Fluorescence image
Cells were seeded in 6-well plates overnight and then transfected GFP-RFP-LC3 adenovirus (Beyotime), after 24h, the medium was removed and replaced with various concentrations of Neferine for another 24 h. Autophagic flux was measured under the fluorescence microscopy (Carl Zeiss).
RNA interference
The sequence of siRNAs against p62 was 5’-GCATTGAAGTTGATATCGAT-3, as previously published[21]. Cells were seeded in six-well plate and transfected with siRNA using Lipofectamine3000 (Invitrogen). After 72 h, the transfected cells in parallel conditions were used for neferine experiments.
Xenograft mice model
The animal experiment was performed according to the Ethics Review Board at the Shanghai Ninth People Hospital. The CAL27 (2×106 cells) suspended in 20% Matrigel (BD Biosciences) were injected to BALB/c nude mice (CRL, China) subcutaneously. The mice were treated with neferine (10mg/kg) and PBS (control) by intraperitoneal administration after a week. The volumes of tumor were measured every four days. The mice were euthanatized and tumor were required at end of the experiment.
Immunohistochemistry staining
The slides were disposed through deparaffinage, rehydration, antigen repairation, the endogenous peroxidase inactivation and nonspecific antigen blocking. The slides were incubated with primary antibody overnight, the secondary antibody 15min. Staining was displayed by a DAB reagent (Zhongshan). The intensity and proportion of staining were scored by 2 pathologists.
Statistical analysis
SPSS version 18.0 software was used for statistical analysis. For each of the 3 independent experiments, data are presented as the mean ± SEM. Statistical comparisons between 2 samples were performed using the Student's t-test and multiple comparison were analyzed by one-way ANOVA test. Differences were considered statistically significant when P<0.05.