Tissue specimens and patients
This study was approved by the Ethics Committee of Harbin Medical University. Samples from 87 cases of histopathologically confirmed invasive ductal breast cancer (IDC) and 48 cases of ductal carcinoma in situ (DCIS) as well as 24 samples of normal breast tissue were included in this study. The IDC patients were female, hospitalized at the Affiliated Tumor Hospital of Harbin Medical University from March 2010 to November 2010 and followed-up until March 2015. The median follow-up was 58.9 months (range 16.8 to 63.3 months). Formalin-fixed paraffin-embedded (FFPE) tissues and complete clinical records of the patients were collected. None of the patients had undergone preoperative chemotherapy or radiotherapy.
Cell culture
The human breast cancer cell lines MDA-MB-231, MCF7, MDA-MB-468, T47D, UACC-812, MDA-MB-453, SKBR-3, and HCC70 and nontransformed breast cell line MCF-10A were obtained from the Cancer Research Institute of Heilongjiang Province, China. MCF7, T47D, UACC-812 and HCC70 cells were cultured in DMEM (Gibco, Carlsbad, CA, USA), whereas MDA-MB-453 and SKBR-3 cells were cultured in RPMI 1640 (Gibco, Carlsbad, CA, USA). All media for the abovementioned cancer cell lines were supplemented with 10% fetal bovine serum (FBS) (PAN) (Gibco, Grand Island, NY, USA) and 1% penicillin-streptomycin (Gibco, Grand Island, NY, USA). MCF-10A cells were maintained in DMEM-F12 (Gibco, Carlsbad, CA, USA) medium supplemented with hydrocortisone (0.5 μg/ml), insulin (10 μg/ml), hEGF (20 ng/ml) and 10% FBS. All cells were cultured in a humidified incubator at 37 °C with 5% CO2. MDA-MB-231 and MDA-MB-468 cells were cultured in RPMI 1640 (Gibco, Carlsbad, CA, USA) supplemented with 10% FBS and 1% penicillin-streptomycin at 37 °C in a humidified incubator without CO2.
Cell transfection
UACC-812 and T47D cells were infected with lentiviruses expressing specific shRNA to knock down GABARAP (GABARAP-shRNA). Human GABARAP targeted RNAi (RNAi: GCCUACAG UGACGAAAGUGTT) sequences was obtained from GeneChem Co. Ltd. (Shanghai, China). As a control, scrambled versions of these sequences(NC: GGCUCUAGAAAAGCCUAUGCdTdT) were used. The sequences shown above were inserted into the GV248 vector plasmid. For overexpression of GABARAP in MDA-MB-453 cells, full-length human GABARAP cDNA was cloned into the pLVX-puro vector. Lentiviral particles were constructed and packaged by Shanghai GeneChem Co. Ltd. Briefly, the cells were infected with lentivirus to generate stable cell lines. After 24 h, the cells were transferred to medium containing 4 μg/ml puromycin and were cultured for 3 days.
Cell viability assay
The proliferation of T47D, UACC-812 and MDA-MB-453 cells proliferation assay was assessed with a Cell Counting Kit-8 (CCK-8) (Beyotime Institute of Biotechnology, Shanghai, China) according to the manufacturer’s instructions. Briefly, 1000–3000 cells per well (depending on the cell type) were plated in each well of a 96-well plate and cultured overnight. CCK-8 reagent (10 μL per well) was added at 24, 48 or 72 h after seeding and incubated at 37 °C for 2 h, at which point the absorbance of optical density (OD) value at 450 nm was measured. Three parallel experiments were performed for each assay with five replicate wells per condition.
Cell invasion assays
For the invasion assays, cells in serum-free medium were seeded into the upper chamber of a transwell insert (8-µm pore size, Millipore) coated with Matrigel (30ul 1:8 dilution, Sigma-Aldrich, USA). Medium containing 10% FBS was added to the lower chamber. After the cells were incubated at 37 °C for 48 h, noninvading cells that remained in the top chambers were removed with a cotton swab, and the cells that had migrated to the underside of the membrane were fixed in 100% methanol for 30 min, air-dried, stained with 0.5% crystal violet (Sigma, St. Louis, MO, USA), imaged, and counted under a light microscope.
Colony formation assay
Cells were seeded into a 6-well plate and cultured for 14 days in medium containing 10% FBS. Colonies were fixed in methanol for 30 min, and 500 μL of 0.5% crystal violet was added to each well for 30 min for visualization and counting.
Wound healing assay
For wound healing assays, cells cultured to 95% confluence in a 6-well plate were scratched with a 10-μL pipette tip. Then, images of the wound were taken at 0 h and 24 h. Mobility was calculated as follows: (mean area at 0 h–mean area at×h)/(mean area at 0 h)×100%.
Immunohistochemistry (IHC)
The detailed experimental immunohistochemical procedures were described previously [25]. Antibodies against GABARAP (Proteintech, 11010-1-AP, dilution 1:100), E-cadherin (Proteintech, 20874-1-AP, dilution 1:4000), p-mTOR (Ser2448; Affinity, AF3308, dilution 1:50), matrix metalloproteinase (MMP) 2 (Proteintech, 10373-2-AP, dilution 1:200) and MMP14 (Proteintech, 14552-1-AP, dilution 1:200)were used for IHC.
Western blot
Cells were lysed using RIPA lysis buffer containing protease inhibitors to obtain protein. A BCA Protein Assay Kit was used to determine the protein concentrations. Proteins were separated by 10% SDS-polyacrylamide gel electrophoresis and transferred to PVDF membranes. Subsequently, the membranes were blocked with 5% BSA blocking reagent for 1 hour at RT and incubated with primary antibodies overnight at 4°C. The next day, the membranes were washed and incubated for 1 hour at RT with secondary antibodies. Finally, the proteins were analysed using the ECL Plus kit. The antibodies used included the following: GABARAP (Abcam, ab109364, dilution 1:1000), E-cadherin (Abcam, ab40772, dilution 1:1000), N-cadherin (Abcam, ab76011, dilution 1:1000), Vimentin (Proteintech, 10366-1-AP, dilution 1:1000), MMP2 (Abcam, ab110186, dilution 1:1000), MMP14 (Abcam, ab3644, dilution 1:1000), AKT (Abcam, ab179463, dilution 1:1000), p-AKT (Ser473; Bioworld Technology, BS4007, dilution 1:1000), mTOR (Abcam, ab2732, dilution 1:1000), p-mTOR (Ser2448; Cell Signaling Technology, 5536, dilution 1:1000), p70S6K (Proteintech, 14485-1-AP, dilution 1:1000), and p-P70S6K (Thr389; Cell Signaling Technology, 9234, dilution 1:1000), MEK1/2 (Cell Signaling Technology, 8727, dilution 1:1000), p-MEK1/2 (Ser217/221; Cell Signaling Technology, 9154, dilution 1:1000), ERK1/2 (Cell Signaling Technology, 4695, dilution 1:1000), p-ERK1/2 (Thr202/Tyr204: Cell Signaling Technology, 4370, dilution 1:1000), IKK-β (Cell Signaling Technology, 8943, dilution 1:1000), p-IKK-β (Cell Signaling Technology, 2078, dilution 1:1000), IκBα (Cell Signaling Technology, 4812, dilution 1:1000), p-IκBα (Cell Signaling Technology, 2859, dilution 1:1000). Equal protein loading was assessed using a mouse anti-β-actin antibody (ZSGB-BIO, TA-09, dilution 1:1500).
Nude mouse tumor xenograft model
BALB/c athymic nude mice (female, 4–5 weeks old) were purchased from Beijing Vital River Laboratory Animal Technology Co., Ltd. and bred in pathogen-free conditions at the Animal Center of the Affiliated Tumor Hospital of Harbin Medical University. UACC-812/vector control or UACC-812/GABARAP-shRNA cells (5×106 cells in 100 µL of PBS) were subcutaneously injected into the left flanks of mice in each group (n=10 per group). When palpable tumors formed, the mice bearing UACC-812 cells with or without stable knockdown of GABARAP were randomized into two subgroups (n=5 per subgroup) and injected with LY294002 (75 mg/kg) or sterile water into the peritoneal cavity twice weekly for 3 weeks. Subsequently, the tumor volume was monitored with Vernier calipers every five days for 3 weeks and calculated using the equation (L ×W2)/2, where L is the length and W is the width. Tumor weight was measured after excision on the final day of the experiment. After all the mice were sacrificed, a portion of the tumor tissue was fixed in formalin and embedded in paraffin for immunohistochemical analysis. All animal experiments were performed in accordance with the Institutional Animal Care and Use Committee (IACUC) of Harbin Medical University in China and the NIH Guidelines for the Care and Use of Laboratory Animals.
Statistical analysis
Statistical analyses were performed with SPSS 22.0 and GraphPad Prism software. The data are expressed as the means ± standard deviations (SDs). All experiments were performed at least three times. The differences between two groups were analyzed with Student’s tests and the χ2 test. The survival analysis was performed using Kaplan-Meier analysis and log-rank tests. Data from The Cancer Genome Atlas Breast Invasive Carcinoma (TCGA-BRCA) cohort were downloaded from the UALCAN Database (http://ualcan.path.uab.edu/index.html) and Oncomine Database (https://www.oncomine. org/resource/login.html); these data sets were used to detect GABARAP mRNA expression and survival analysis in breast cancer. A two-tailed p value < 0.05 was considered significant.