Bioinformatic methods and data analysis. Data derived from 1,211 breast cancer samples (including 114 normal breast tissues and 1097 cases of primary breast tumor) and 833 breast cancer samples (which divided into four groups based on their histological subtype) were downloaded from The Cancer Genome Atlas (TCGA) database (https://cancerge nome.nih.gov). Correlation analysis was conducted through Gene Expression Profiling Interactive Online Analysis (http://gepia.cancer-pku.cn/index.html) in TCGA breast cancer datasets by Pearson's correlation analysis method (Pearson's r = 0.5; P = 0).
Cell culture
ER-positive human breast cancer cell lines (MCF7 and T47D), and MCF7 and T47D derived tamoxifen-resistant cell lines (MCF7R, T47DR), were grown in RPMI 1640 medium containing 1% double antibody with 10% fetal bovine serum and cultured at 37°C in a standard incubator with 5% CO2.
Plasmids and siRNAs. Synthetic small interfering RNA (siRNA) was used to temporarily knock down PKIB (RiboBio, Guangzhou, China). Short hairpin RNA (shRNA) oligonucleotides (GenePharma, Shanghai, China) were used to generate stable PKIB knockout cells via lentivirus-mediated transduction according to the manufacturer's protocol.
Antibodies and reagents. The antibodies used for Western blots in this study included: anti-PKIB (ab233521, Abcam, 1:1000), anti-ATG7 (67341-1-Ig, ProteinTech, 1:100), anti-pCREB (9198S, Cell Signaling Technology, 1. 1000), anti-CREB (9197T, Cell Signaling Technology, 1. 1000) LC3I II (9116, Cell Signaling Technology, 1: 1000), anti-Lamin-B1 (17416S, Cell Signaling Technology, 1: 1000), anti-β-actin (66009-1-Ig. ProteinTech, 1:1000), anti-SQSTM1 (66184-1-Ig, ProteinTech, 1:1000). Autophagy inhibitors and autophagy agonists were purchased from MCE Biosciences Inc. Tamoxifen was from Sigma.
Cell lines and transfection. Tamoxifen-resistant cell lines were constructed using a low-concentration continuous induction method according to the literature (25, 26). MCF7 and T47D were purchased from ATCC. siRNA transfection was performed using Lipofectamine 3000 transfection reagent (Invitrogen) according to the manufacturer's instructions. Stable clones were selected and maintained in 2 mg/mL of puromycin (Sigma) for PKIB knock down of shRNAs.
Quantitative RT-PCR. Total cellular RNA was extracted by the Trizol method and cDNA was formed using the Reverse Transcription Kit(Thermo Fisher Scientific). The expression of genes was calculated according to the method mentioned in the literature.(15).
Western blot analysis. Cells were washed twice with sterile pre-cooled PBS before harvested, added cell lysis solution (Beyotime, China) and protease inhibitor. Centrifuged at 12,000rpm for 30min at 4°, remove supernatant. Protein concentration were assessed via BCA method. Protein samples were subjected to 12.5% SDS-PAGE and transferred to PVDF membranes (Bio-Rad, USA). The membranes were then blocked with 5% skim milk in 0.1% TBST buffer at 4°C overnight. The membranes were subsequently incubated with PKIB (ab233521, Abcam, 1:1000), ATG7 (67341-Ig, ProteinTech, 1:100), p-CREB1 (9198S, Cell Signaling Technology, 1:1000), CREB (9197T, Cell Signaling Technology, 1. LC3I II (9116, Cell Signaling Technology, 1:1000), Lamin-B1 (17416S, Cell Signaling Technology, 1:1000), β-Actin (66009-1- Ig, ProteinTech, 1:1000), and SQSTM1 (66184-1-Ig, ProteinTech, 1:1000). Protein-antibody complexes were detected using HRP-conjugated secondary antibodies and enhanced chemiluminescence (Pierce). Band intensities were quantified using ImageJ software (NIH, Bethesda).
Immunofluorescence and confocal microscopy. The cells were seeded onto coated cover slips, fixed with 4% paraformaldehyde for 15 min at room temperature, treated with 0.1% Triton X-100, and blocked with 5% normal goat serum. They were then incubated with primary antibodies overnight at 4°C, washed thrice in phosphate-buffered saline (PBS), and stained with an FITC-labeled goat anti-rabbit secondary antibody (1:200; Zhongshan Golden Bridge); DAPI was used as the nuclear stain. Immunofluorescence images were taken using a confocal microscopy (Cal Zeiss, Zeiss LSM510 Meta). The LC3B-puncta in each cell were counted (10 fields per sample are indicated). Data obtained from 1 of 3 independent experiments with similar results were presented
Small interfering RNA studies. The cells were planted in serum-free medium without antibiotics at 2 × 104 per well on a 24-well plate. They were then transfected with 50 nmol/L negative control small interfering RNA (siRNA), or 50 nmol.L− 1 PKIB siRNA (RiboBio, China) using Lipofectamine® RNAi MAX Transfection Reagent (Life Technologies, USA). The medium was changed after 6 h and every other day thereafter until the end of the experiment.
Transmission electron microscopy. For transmission electron microscopy assay, cells samples were prepared as previously described(29) ,and then were examined with an electron microscope (JEOL, JEM-1010).
Animal experiment. All in vivo experiments were conducted using 4–6 week old female nude mice. All animal experiments were approved by the Laboratory Animal Care and Use Committee of Chongqing Medical University. The 4–5 week old female Balb/c nude mice were pre-treated with subcutaneous estrogen injections one week prior to inoculation of tumour cells. The amount of tumour cells inoculated was 1 x 107, (including MCF7/sh-PKIB cells or MCF7/sh-NC cells) and sterile PBS solution and stromal gel were prepared in a 1:1 ratio to make a 100ul solution to fully resuspend the tumour cells.After inoculation, tumour formation in nude mice was regularly observed, and when tumours were palpable, tumour size was regularly measured and tumour volume was calculated using the following formula: tumour volume (mm3) = length x width 2 x 0.5. When tumour volume reached or exceeded 100 mm3, MCF7/sh-PKIB or MCF7/sh-NC xenograft mice were divided into three groups (5 mice per group) as follows. The details are as follows. (1) control group (PBS), (2) tamoxifen group (ip, 4 mg/kg, twice weekly), and (3) tamoxifen + HCQ group (Tam, ip, 4 mg/kg, twice weekly; HCQ, ip, 5 mg/kg). Tumour volumes were continuously measured until 2 weeks after the complement of treatment. Mice were humanely executed and tumour tissues were collected for immunohistochemical staining.
Immunohistochemistry. Paraffin blocks of prepared mouse tumour tissue were cut into thin slices of 4 µm thickness. Antigen retrieve was performed in 0.01 M citrate buffer (pH 6.0) for 30 minutes in an autoclave, followed by treatment with 3% hydrogen peroxide for 15 minutes. Specimens were closed with 10% goat serum for 1 hour at room temperature. Samples were incubated overnight at 4°C with antibodies specific for PKIB, ATG7 and pCREB1. Immunostaining was performed using DAB (Dako) according to the manufacturer's instructions. Immunohistochemical sections were placed under a 200X microscope with 5 randomly selected fields of view, images were saved and the mean expression intensity was calculated using Image J software 6.0. Two independent pathologists in our hospital analyzed the staining results
Cell viability. Cell proliferation was detected using the Cell Counting Kit-8 (Boster Biological Technology co.ltd), according to the manufacturer’s instructions. 4000 cells/well were seeded into a 96-well plates, then were incubated at 37°C. 10 µL of CCK-8 solution was added and the cells incubated at 37°C for 2 h before the absorbance was determined by Multiskan Spectrum 1500 (Thermo Scientific, PA) at 450 nm.
Sample collection. Twenty paired human primary breast cancer specimens and recurrent tumor tissues were surgically obtained from the Department of Endocrine Breast Surgery, at the First Affiliated Hospital of Chongqing Medical University, and frozen at -80°C. Written informed consent was obtained from each patient. The Ethics Committee of the First Affiliated Hospital of Chongqing Medical University approved this study.
Statistical analysis. Survival curve analysis was carried out through Kaplan-Meier plotter (http://kmplot.com/), an online survival analysis platform. All experiments were performed independently at least three times. Statistical analysis was conducted using the SP2222.0 standard software package (Chicago, USA) and in vitro experiments were reread three times and the results expressed as mean ± SD. Data between two independent sample groups were analysed using t-tests, data between multiple samples were analysed using ANOVA tests, and data on categorical variables were analysed using chi-square or fisher's exact probability tests, and were considered statistically different when p < 0.05.