Cell lines, tumor samples and normal tissues
Cell lines (Hela, CaSki, HEK293T) were obtained from the American Type Culture Collection (ATCC, Manassas, VA, USA) and collaborators. Cancer cell lines (Hela, CaSki) were cultured in RPMI 1640 medium (Gibco-BRL, Karlsruhe, Germany) with 10% fetal bovine serum (FBS), and 293T cells were grown in high glucose DMEM (Gibco-BRL, Karlsruhe, Germany) supplemented with 10% FBS. All cells were cultured at 37 °C in a humidified atmosphere containing 5% CO2.
All tissue samples used were acquired from the First Affiliated Hospital of Chongqing Medical University, including primary tumor and paired surgical margin tissues as well as normal tissues. In order to make sure that the percentage of tumor cells was over 70%, tissue samples were pathologically and histologically examined with collection of clinical and pathological data followed. This study was conducted according to provisions of the Helsinki Declaration in 1975 and authorized by the Institutional Ethics Committees of the First Affiliated Hospital of Chongqing Medical University (Approval notice: No.20180305).
Construction of plasmids and transfection
To construct the ZBTB28 expression plasmid, the homo sapiens ZBTB28 full-length gene with a HA-tag was cloned into the pcDNA-3.1(+) framework plasmid. The recombinant plasmids were transformed into E.coli DH5a cells (CB101,TIANGEN) and then sequenced. Cells were transfected with plasmid DNA using Lipofectamine 2000 reagent (Invitrogen) according to the manufacturer’s instructions. Stably transfected pcDNA-3.1 and pcDNA-ZBTB28 cells were acquired by G418 selection (600 μg/ml for CaSki, 800 μg/ml for HeLa).
RNA isolation, Reverse transcriptase-PCR and Real-Time PCR
Learning from the manufacturer’s instructions, total RNA was isolated from cell lines and clinical samples using TRIzol Reagent® (Molecular Research Center, Cincinnati, OH, USA). 20 μl cDNA was synthesized from 1 μg RNA by Reverse transcriptase-polymerase chain reaction (RT-PCR). Real-time PCR was performed by using Go-Taq (Promega, Madison, WI, USA) under the following conditions: initial denaturation at 95 ℃ for 2 min, followed by 32 cycles (95 ℃ for 30 s, 55 ℃ for 30 s and 72 ℃ for 30 s) of amplification, and final extension at 72 ℃ for 3 min. β-actin was amplified as a control and with 23 cycles. Semi-quantitative RT-PCR, with β-actin as a control, was put into practicing with Go-Taq DNA polymerase (Promega) and performed by using a final volume of 10μL reaction mixture that contained 2 μL cDNA. The amplified products were electrophoretic in 2% agarose gel to detect the target bands. In the case of SYBR Green (Thermo Fisher), Real-time quantitative PCR had performed. With the action of 7500 Real-Time PCR System (Applied Biosystems, Foster City, CA, USA), all analyses were performed. The primer sequences are shown in Table.S2 and Table.S3.
5-Aza-2’-deoxycytidine (5-Aza) treatment
CaSki and Hela cell lines were treated with 10 μmol/L 5-Aza (Sigma-Aldrich, Steinheim, Germany), a demethylation agent, for 4 days. Then cells were harvested for qRT-PCR analysis.
Bisulfite treatment, methylation-specific PCR (MSP) and quantitative methylation specific PCR (qMSP)
To evaluate ZBTB28 methylation status, bisulfite modification of DNA was performed [26]. By using AmpliTaq-Gold DNA Polymerase (Applied Biosystems), MSP was then exercised with methylation-specific primers to specifically recognize unmethylated or methylated ZBTB28 gene sequences. Products were electrophoresis with 2% agarose gels (MBI Fermentas, Vilnius, Lithuania) and recorded on a gel imaging system (Bio-RAD Gel Doc XR+, CA). The primers of qMSP were mentioned before [7].
Tumor xenograft model and metastasis models in nude mice
All animal experiments in this study were conducted in compliance with animal protocols approved by the Experimental Animal Center of Chongqing Medical University, and were approved by the institutional ethics committee of the First Affiliated Hospital of Chongqing Medical University, China. Six BALB/c nude mice (aged 4–6 weeks, weighing 18–22 g) were purchased from Beijing Vital River Laboratory Animal Technology Co. Ltd. Stable ZBTB28- expression Hela cells or control cells (5 × 106 cells were resuspended in 100 ul PBS) were injected into subcutaneous tissues on both sides of the back of 6 nude mice. The primary tumor size was measured on the fourth day after injection. The second measurement was performed on the eighth day. And then measurements had been taken every two days until the 18th day after injection. The longest and the shortest diameters of tumors were measured using vernier calipers, and tumors’ volume (mm3) were calculated as follows: volume = length × width2 × 0.52. All nude mice were euthanized the 19th day after injection, and their tumors were collected and weight. Some of the collected tumor tissues were used for embedding sections, and some were frozen in -80 ℃ refrigerator for subsequent experiments. As previously described [27], female BALB/c nude mice (5–6 weeks) were used in metastasis assays. Two weeks after tail vein injection, the mice were sacrificed and checked for lung metastasis using standard histological examination (Approval notice: No.20180226).
Flow cytometry (FCM)
Cell cycle arrest and apoptosis were assayed by flow cytometry (FCM). For cell cycle analysis, stably transfected cells were harvested with trypsin, then washed twice with PBS, suspended with ice-cold 75% ethanol and fixed overnight. The next day, cells added with RNA enzyme were incubated at 37 ℃ for 30 min, and stained with propidium iodide (PI) for 30 min in dark to assay for cell cycle distribution. In order to analyze apoptosis, transiently transfected cells were double staining with annexin V-fluorescein isothiocyanate and PI. A Cell Quest kit (BD Biosciences, CA, USA) was employed to assess FCM results.
Cell proliferation (CCk8)
CaSki and Hela cells were cultured in 96-well plates at a density of 3000 cells/well after transfection with ZBTB28-expressing or control (pcDNA3.1) plasmids. The absorbance of cells in each well at 450 nm was measured with CCK8 kit at 0 h, 24 h, 48 h, 72 h, and the mean value of each well was obtained after testing nine times.
For the half maximal inhibitory concentration (IC50) determination, cells were treated with progressively increased concentrations of drugs for 72 h. Cisplatin (HY-17394), Paclitaxel (HY-B0015) and 5-FU (HY-90006) were purchased from MedChemExpress. The value of IC50 was calculated by nonlinear regression analysis with software program GraphPad Prism version 5.
Colony formation assays
Stably transfected pcDNA-3.1 and pcDNA-ZBTB28 cells (CaSki and Hela) were plated in six-well plates (200 cells/well). After 12 day, cells were fixed with 4% Paraformaldehyde (PFA) for 30 min and stained with gentian violet (Beyotime Institute of Biotechnology, Shanghai, China). Photographed with a phase contrast microscope (Leica DMI4000B, Milton Keynes, Buckinghamshire, UK), colonies with more than 50 cells were manually counted with Photoshop software.
Transwell® assays for cell migration and invasion
For Transwell® assays, the chambers (8 μm pore size, BD Sciences, Bedford, MA) with or without Matrigel (100 μg/ml, BD Biosciences, San Jose, CA) were used to get assessment to cell migration and invasion capacities. For migration assay, collected cells were washed twice in serum-free medium and added to the upper compartment (3 × 104 cells). The lower chamber contained 700 μl RPMI 1640 medium containing 20% fetal bovine serum (FBS). For invasion assay, the matrix gel was precoated on the upper compartment. After incubation for 48 h, cells were fixed with 4% paraformaldehyde for 30 min and stained for 30 min with crystal violet. Non-migratory cells on the upper side of the chamber were wiped away gently. Photographed with a phase-contrast microscope (Leica DMI4000B) after fixation and staining, migrated cells were counted. five fields of view were randomly selected for counting.
Immunofluorescence and Western Blot
Immunofluorescence was performed as previously described [28]. Cells grown on round coverslips were incubated with HA-tag (#3724, Cell Signaling Technology), anti-Vimentin (sc-6260, Santa Cruz), and anti-E-cadherin (#14472, Cell Signaling Technology) antibodies and secondary antibodies conjugated with Alexa Fluor 488 and 594. Nuclei were counterstained with DAPI (C1006, Beyotime Biotechnology, Haimen, China). Images were acquired on a fluorescence microscope (Olympus, Tokyo, Japan) using 40 × objective.
Western blot was performed to determine the levels of the autophagic proteins p62 (#8025, Cell Signaling Technology), LC3 (ab128025, abcam), apoptosis proteins Cleaved Caspase8 (WL00659, Wanleibio, China), PARP and Cleaved PARP (WL01932, Wanleibio, China), Caspase 3 and Cleaved Caspase3 (WL02117, Wanleibio, China), EMT proteins Occludin (TA306787, OriGene Technologies), Vimentin (sc-6260, Santa Cruz), N-cadherin (610921, BD Biosciences) and other primary antibodies HA-tag (#3724, Cell Signaling Technology), Bcl-XL (sc-8392, Santa Cruz), BECN1 (sc-48341, Santa Cruz), FIP200 (PA5-69698, Thermofisher). The β-actin (sc-8432, Santa Cruz) which was kept as an internal control in CaSki/HeLa cells during the course of differentiation with or without the presence of CQ or overexpression of ZBTB28. Moreover, EMT related proteins (N-cad and VIM) were also detected. Equal amounts of protein (40 μg) were separated by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and transferred onto polyvinylidene difluoride (PVDF) membranes (Bio-Rad, Hercules, CA, USA). Autophagy inhibitor CQ (HY-17589A) and 3MA (HY-19312) were purchased from MedChemExpress.
The membranes, was firstly blocked with PBST (PBS containing 0.1% Tween 20) containing with 5% nonfat dry milk at room temperature for 2 h and then washed with PBST for three times, secondly incubated with the primary antibody at 4 ℃ overnight and then washed with PBST. After that, membranes were incubated with the corresponding secondary antibody (BL001A, BL003A, Biosharp, China) at room temperature for 45 min and then washed with PBST for another 30 min. Protein bands were visualized by Immobilon Western Chemiluminescent HRP Substrate kit (Millipore Corporation, Billerica, MA, USA), and the band detections were within the linear range.
ChIP assay
Chromatin immunoprecipitation (ChIP) analysis was performed according to the manual of the SimpleChIP® Enzymatic Chromatin IP Kit (#9003, Cell Signaling Technology). Stably ZBTB28-expressing CaSki/HeLa cells and vector-expressing cells, first were washed with RPMI 1640 medium, then were washed with ice-cold PBS devoid of Ca2+ and Mg2+ and supplemented with a protease inhibitor cocktail (PIC, P8340, Sigma-Aldrich). Afterwards in order to terminate the reaction, DNA and protein were cross-linked with 1% formaldehyde for 10 min at room temperature followed by 0.125 M glycine for 5 min. Then cells were lysed in lysis buffer (20 mM Tris-HCl, pH 8.0, 50 mM NaCl, 5 mM CaCl2, 1% Triton X-100, PIC) for 10 min and micrococcal nuclease was added for 20 min at 37 °C. In order to acquire 200–900 bp DNA fragments, cells were sonicated on ice of 9 sec pulses at 30% amplitude with an ultrasonic cell disruptor (JY88-IIN, Scientz, China) at an interval of 1 min for five sets. The remanent diluted samples, whose lysates was removed 10 µl in advance to serve as an input sample, were incubated with HA-tag antibody (#3274, Cell Signaling Technology) overnight at 4 °C, followed by capture with protein A/G magnetic beads (#9006, Cell Signaling Technology) for 2 h at 4 °C. Rabbit anti-histone H3 antibody (#4620, Cell Signaling Technology) and normal rabbit IgG (#2729, Cell Signaling Technology) were respectively used as positive and negative controls. As recommended, the complexes were precipitated, washed, and eluted. After DNA-protein cross-linkages were incubated with 6 μl of 5 M NaCl and 2 μl of proteinase K at 65 °C overnight, DNA was washed and purified with Anhydrous ethanol for once, 75% ethanol for 2 times, then drying at 55 ℃ for 10 min. 50μl of enzyme free water was added for further using in q-PCR analyses. The primer sequences are shown in Table.S4.
Autophagy flux assay
For the autophagy assay, CaSki and Hela cells were imaged by confocal laser scanning microscope, after transfected with eGFP/eGFP-LC3 for 48 hours.
Transmission Electron Microscopy (TEM)
The cells were stained with uranyl acetate/lead citrate and observed by a Hitachi H-7650 transmission electron microscope (Tokyo, Japan) operated at 100 KV.
Luciferase reporter assay
293T, CaSki and HeLa cells were seeded in 24-well plates and grown to 50-60% confluence. Then the cells were co-transfected with pGL3-gene, HA-ZBTB28, and monitor plasmid pRT-LK (80:1 ratio). After 48 hours, the cells were lysed in 100 μl lysis buffer and the Firefly and Renilla luciferase activities were detected by the Dual-Luciferase Reporter System (Promega) according to the manufacturer's instructions. After the luciferase activity of the tested sample had been normalized, data are represented as the fold induction to that of the corresponding control sample.
Spheroid forming assay
Spheroid culture was performed as previously described [7]. Briefly, 2000 cells were seeded onto 6-well plate, after 2 weeks, the spheroids were examined using microscope (Olympus, Tokyo, Japan). The number of spheroids was calculated using captured images. Spheroid cells larger than 50 µm were considered as formed spheroids. The efficiency of spheroid formation is the percentage of spheroid cells in live cells seeded.
Acridine orange (AO)/ethidium bromide (EB) staining
AO/EB double staining was used to detect apoptosis (A simple technique for quantifying apoptosis in 96-well plates). Briefly, 5000 cells/well were seeded in a 24-well plate. After 24 hours, gently washing with 1× PBS, then the cells were stained with acridine orange (100 μg/ml) and ethidium bromide (100 μg/ml) mixed solutions for 1 min(kit). After staining the cells were washed with 1× PBS, then observed under a microscope (Olympus, Tokyo, Japan) and recorded.
EdU (5-ethynyl-2’-deoxyuridine) incorporation assay in vitro
EdU detection was performed using the BeyoClickTM EdU Cell Proliferation Kit with Alexa Fluor 488 (Beyotime Biotechnology, Haimen, China), according to manufacturer’s instructions. In brief, cervical cancer cells were incubated with 10 µM EdU for 2 h at 37 °C. Cells were then fixed with 4% paraformaldehyde and permeabilized with 0.3% Triton X-100 for 15 min at room temperature. Next, the fixatives were removed, and the cells were washed with PBS containing 3% BSA (4240GR005, BioFroxx). Last, cells were incubated from light in Click Additive Solution for 30 min then stained nucleus with Hoechst. The pictures of EdU detection samples were then acquired under microscope (Olympus, Tokyo, Japan) and photographed. The cell proliferation was further analyzed by counting the ratio of EdU incorporated cells to the total number of cells.
Immunohistochemistry (IHC)
Briefly, paraffin sections were dewaxed, washed twice in absolute ethanol, follow the instructions (ZSGB-BIO, SP9000) for hydration and antigen retrieval. Next, incubated slides with reagent 1 for 10 min at room temperature to inactivate endogenous peroxidase, and followed by three times washes in PBS for 3 min. Then sections were incubated in blocking solution (Reagent 2) for 15 min, continued by overnight incubation at 4 °C with PCNA (#13110, Cell Signaling Technology), HA-tag antibody in immunohistochemical wet box. Next day, sections were three washes with PBS, then incubated with reagent 3 at 37 °C for 30min in wet box, washed again in PBS, and incubated with reagent 4 at 37 °C for 30min. After three times washed with PBS, immunolabeling was performed with 1x diaminobenzidine (DAB, ZSGB-BIO, ZLI-9018). Finally, the sections were counterstained with hematoxylin (BL702B, Biosharp, China).
siRNA and transfection
siRNA sequences against human BECN1 and FIP200 were purchased from OriGene (OriGene Technologies, Rockville, MD). At a concentration of 10 nM, a pool of three different siRNA duplexes was used to transfections. Transient transfections were performed in 6-well plates using Lipofectamine 2000 (Invitrogen). After transfection 48-72 h, cells were harvested for subsequent assays.
Statistical analyses
GraphPad Prism 5 was used to conduct the statistical analysis. All data were presented as the mean ± standard error of the mean (SEM). Statistical analysis was performed by comparing two groups of data in the way of Student t test. The significance of statistical analysis was clarified by *p <0.05, **p <0.01 and ***p < 0.001.