Clinical tumor specimens
Primary breast cancer specimens were obtained from the tissue bank at the Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China. Formalin-fixed paraffin-embedded (FFPE) primary tumor specimens of IMPC (n = 124, from Jan 2007 to Dec 2012) and the period corresponding to IDC-NST (n = 149) were diagnosed by three independent pathologists. No patients included in this study received any chemotherapy or radiotherapy before the surgery, and their complete clinical data were available. The histologic type determination was based on the tumor-node-metastasis (TNM) staging system, reclassified according to the World Health Organization (WHO) classification. The date of death and the date of relapse were used to calculate overall survival (OS) and disease-free survival (DFS). OS was calculated from diagnosis to the date of death. DFS was defined as the time from diagnosis to disease progression or death, regardless of which occurred first. In IMPC patients, with a median follow-up of 72 months, recurrence or distant organ metastasis was observed in 33 patients, and 22 patients died. This study was approved by the Ethics Committee of Tianjin Medical University Cancer Institute and Hospital.
Cell lines and culture
Breast cancer cell lines (MCF-7, T47D, BT474, MDA-MB-231), HEK293 and HEK293T cells were used in this study. The cell lines were purchased from American Type Culture Collection (ATCC, Manassas, USA). Cells were cultured according to the manufacturer’s protocols. As their phenotypic characteristics and patterns of genomic copy number variation (CNV) are consistent with those of the IMPC specimens [21], the ER-positive breast cancer cell lines MCF-7, T47D and BT474 were used in this study. All cells were cultured at 37 °C and 5% CO2.
miRNA in situ hybridization and protein immunohistochemical analysis
miRNA in situ hybridization (ISH) procedures were conducted as previously described [22]. Tumor sections were digested with proteinase K for 10 min and hybridized with hybridization solution at 54 °C for 2 h with double-DIG-LNA probes for miR-30c, U6 (positive control) or scrambled RNA (negative control) (Exiqon, Denmark) (Supplementary Fig. S1). After washing with PBS, the slides were incubated with sheep anti-DIG-AP (Roche, Switzerland) and then stained with nitroblue tetrazolium/5-bromo-4- chloro-3-indolyl-phosphate (Roche, Switzerland). Nuclear Fast Red was used to counterstain the nuclei. A positive signal appeared blue in the cytoplasm and nucleus. The intensities of miR-30c staining were scored as 0–4, according to previously described standards [23].
Immunohistochemical staining was performed on FFPE tissue sections. The sections were incubated with primary antibodies against MTDH (Invitrogen 40-6500, USA), MUC1 (Abcam ab45167, England), Vimentin (Cell Signaling Technology 3932, USA), N-cadherin (BD Biosciences 610920, USA), E-cadherin (Cell Signaling Technology 3195, USA), and Ki67 (Thermo Fisher Scientific RM9106S0, USA) overnight at 4 °C. Then, the sections were treated with biotinylated antibody, streptavidin-biotin-peroxidase and DAB complex (Beijing Zhongshan Biotechnology, China). The nuclei were counterstained with hematoxylin. The intensities of MUC1 and MTDH staining were scored between 0 and 4 as previously described [24, 25].
Vector construction and lentivirus production
MTDH 3’UTR fragments containing miR-30c putative targeting sites were subcloned into the firefly luciferase 3’UTR. Point mutations of miR-30c targeting sites were generated by a plasmid site-directed mutagenesis kit (Takara, Japan).
The pLKO.1-puro empty vector and plasmids containing shRNA against MTDH were purchased from Sigma. Lentiviral particles were produced in HEK293T cells by cotransfecting the cells with pLKO.1, pMD2.G and psPAX2 plasmids using Lipofectamine 2000 reagent (Invitrogen, CA) according to the manufacturer’s protocol.
Cells were cultured in 24-well plates with a transfection complex. Approximately 5 µl of 20 µM chemically synthesized miR-30c mimic, miR-30c inhibitor or negative siRNA control was used. Ectopic expression of miR-30c, MTDH and MUC1 was achieved by infection with lentiviral solution (GenePharma, China) along with vector control lentiviral supernatant containing 5 µg/ml polybrene (Sigma, USA). After the cells reached 90% confluency, 2 µg/ml puromycin (Sigma, USA) was added to the medium for 3–5 days to select cells with stable overexpression. Stable cells were maintained in medium containing 1 µg/ml puromycin.
Western blots
Cells were washed with PBS twice, and then proteins were extracted, separated by 10% SDS PAGE electrophoresis and transferred to PVDF membranes (Millipore, USA). To block nonspecific binding, the membranes were incubated with 5% skim milk for 1 h at room temperature. The membranes were then incubated overnight at 4 °C with an antiserum containing antibodies against MTDH (Invitrogen 40-6500, USA), MUC1 (Abcam ab45167, England), β-actin (Sigma-Aldrich A2228, USA), and p-p65 (Abcam 3033, England). WesternBright ECL (Advansta, CA) was used following standard protocols, and blots were imaged with the ImageQuant LAS 4000 luminescent image analyzer (General Electric, CT).
Dual luciferase reporter assay
HEK293 cells seeded in 24-well plates were cotransfected with 500 ng firefly luciferase reporter vector containing the MTDH 3’UTR (named psiCHECK2-MTDH-3’UTR wt) or MTDH 3’UTR mutant (named psiCHECK2-MTDH-3’UTR mut) and 100 nM of negative control siRNA or miR-30c mimics in a final volume of 0.5 ml using Lipofectamine 2000 (Invitrogen, USA). Firefly and Renilla luciferase activities were measured consecutively using dual luciferase assays (Promega, WI) 48 h after transfection. All transfection experiments were performed in triplicate and reproduced at least three times.
SRB assay and colony formation assay
Transfected cells were plated into 24-well plates at 5 × 104 cells/well and cultured for different times. Cells were then fixed and stained with sulforhodamine B (SRB). For the colony formation assay, transfected cells were seeded in 6-well plates at 5000 cells per well. Fourteen days later, colonies were fixed with 4% paraformaldehyde and stained with crystal violet for 15 min.
Cell invasion and migration assay
The migration assay was performed using a Transwell system (24-well, 8 µm pore size with polycarbonate membrane; Corning Costar, USA) according to the manufacturer’s protocol. The invasion assay was performed in the same way as the migration assay except the polycarbonate membranes were coated with 50 µl growth factor-reduced Matrigel (BD Biosciences, USA) at 37 °C for 1 h to form a reconstituted basement membrane. Then, 800 µl serum-containing (20% FBS) medium in each well was added to the lower well of each chamber. A total of 1 × 105 resuspended cells were added to the upper inserts with 100 µl serum-free medium. After 48 h, the remaining cells on the upper side of the Transwell device were removed, and the invading cells at the bottom of the Transwell were fixed with 4% paraformaldehyde and stained with crystal violet.
For wound healing assays, transfected cells were grown in complete medium, and 10 µl pipette tips were used to create an artificial wound in 24-well plates. Cells were washed with PBS to remove the debris and were cultured for 24 h to allow wound healing.
Mouse xenograft model
The animal experiment was approved by the Animal Care and Use Center of Nankai University, Tianjin, China. 17β-Estradiol pellets (0.72 mg, 90-day release; Innovative Research of America, FL) were implanted subcutaneously in the shoulder region of each 4-week-old female BALB/c nude mouse (Charles River, China) one day before cell inoculation. MCF-7 cells (1 × 107) transfected with lenti-miR-30c or lenti-empty were resuspended in a solution of Matrigel (BD Biosciences, USA) or PBS (equal volume), respectively, and then inoculated subcutaneously into the flanks of BALB/c nude mice (n = 12). Tumor volumes were measured once a week and calculated as follows: A × B2/2, where A is the largest diameter and B is the diameter perpendicular to A. Mice were sacrificed eight weeks after injection, and tumors were surgically removed, weighed, and fixed in 4% formalin. H&E staining was performed for histological examination.
To evaluate the effect of miR-30c on tumor metastasis, 1 × 106 MDA-MB-231 cells infected with lenti-miR-30c or lenti-empty were injected into the tail veins of four-week-old female BALB/c nude mice (seven mice for each group). Four weeks later, the numbers of micrometastases in the lung per H&E stained section from individual mice were analyzed by morphological observation.
Three-dimensional (3D) morphogenesis assays
A three-dimensional (3D) morphogenesis assay was performed as previously described (26). Eight-well chamber slides were loaded with 50 µl of growth factor-reduced Matrigel (BD Biosciences, CA) and allowed to set for 1 h. A total of 5000 treated cells/well were then overlaid onto the gel in DMEM supplemented with 10% FBS and 2% Matrigel and cultured for two weeks for counting using an inverted microscope.
Statistics
Statistical analyses were performed using GraphPad Prism 5 software (GraphPad, CA) and the SPSS 21.0 software package (SPSS Inc, USA). Clinicopathological variables between the IMPC and IDC-NST groups were analyzed using the Chi-square test. Correlations between miR-30c, MTDH or MUC1 expression and clinicopathological variables were evaluated by Mann-Whitney U-test and Spearman’s rank correlation analysis. OS and DFS rates were estimated by Kaplan-Meier analysis. Cox proportional hazard regression analysis was performed for the identification of relevant prognostic factors. For tumorigenesis experiments, tumor sizes or weights between two groups were analyzed using Student’s t test. The statistical analysis was two-sided, and P-values less than 0.05 were considered statistically significant.