Cell lines and cell culture
MDA-MB-231, BT474, SUM149, and 293T cells were purchased from American Type Culture Collection (ATCC). Cells were cultured in Dulbecco's modified Eagle's medium (DMEM, 12800-017; Gibco, Grand Island, NY, USA) containing 10% fetal bovine serum (FBS, 10099-141; Life Technologies, Carlsbad, CA, USA), 100 U/mL penicillin, and 100 mg/mL streptomycin in a humidified 5% CO2 atmosphere at 37 °C.
Plasmid construction and generation of stable cell lines
The lentivirus-based vector pLOX/EW-IRES-EGFP [31] was used for ectopic SOX4-expression. SOX4 cDNA was ligated to the Sma I site of the vector and the construct was confirmed by sequencing. The SOX4-expressing vector or the control vector was co-transfected into the 293T packing cells with pAX2 and pMD2G and the lentivirus was collected for subsequent infection into MDA-MB-231 and SUM149 cells. Stably SOX4-expressing cells (MDA-MB-231-SOX4 and SUM149-SOX4) and corresponding control cells (MDA-MB-231-VECT, SUM149-VECT) were sorted using flow cytometry by BD FACS Aria (Becton Dickinson, Franklin Lakes, NJ, USA). For SOX4 knockdown, lentivirus-based pLKO.1-TRC-puro constructs containing a SOX4 short hairpin RNA (shRNA NT or #13-#17) were purchased from Open Biosystems (Huntsville, AL, USA). The lentivirus was prepared as above and used to infect BT474 cells. Stably SOX4-knockdown cells (BT474-14, BT474-16) and control cells (BT474-NT) were yielded after treatment with puromycin (Sigma, San Francisco, CA, USA) for 14 days. To introduce luciferase into tumor cells for bioluminescent imaging in vivo, pMig-Luc-mCherry, pUMVC and pMD2G were co-transfected into the 293T packing cells and the retrovirus was collected to infect tumor cells for xerograph experiments.
Western blot
The protein lysate was resolved by SDS-PAGE and transferred to PVDF membrane. After blocking with 5% bovine serum albumin (BSA), the membrane was incubated with the primary antibody overnight at 4 ºC, followed by incubation with the secondary antibody at room temperature for 1 h. The antibodies used in this study included anti-SOX4 (Cat#H00006659-A01, Abnova, Taipei), anti-GAPDH (Cat#MA5-15738, Invitrogen, Grand Island, NY, USA), horseradish peroxidase (HRP)-conjugated goat anti-mouse IgG (H&L) (Cat#G21040, Invitrogen), and HRP-conjugated goat anti-rabbit IgG (H&L) (Cat#31460, Invitrogen).
MTT assay
Cells were seeded in 96-well plates at a density of 6×106 cells per well and incubated at 37 ºC in humidified 5% CO2 for 24 h. The cells were stained with MTT (Cat#CT02, Sigma) at each time point for 1 h at 37 °C. The absorbance was measured at 490 nm using a spectrophotometer (Bio-Rad, Hercules, CA, USA). For the analysis of resistance to chemotherapeutic agents, carboplatin, adriamycin, 5-fluorouracil, or paclitaxel at different concentrations was added at the beginning of the cell culture which was carried out for 48 h.
Transwell assay
Migration was measured using Matrigel-free Transwell plates (Corning, Midland, MI, USA) with an 8 μm porous membrane. For invasion assay, membrane of the upper chambers was coated with Matrigel (BD Biosciences, Sparks, MD, USA) before use. In total, 1×105 cells were plated in the upper chambers of the Transwells. After a 24-h incubation, migrating or invading cells were stained with 0.5% crystal violet, then photographed at 200x and counted in five random fields. CXCR7 inhibitor CCX771 was a courtesy from ChemoCentryx (Mountain View, CA, USA).
RT-qPCR
Total RNA was prepared with the Trizol reagent according to the manufacturer’s instructions (Invitrogen). cDNA was synthesized using SuperScript Kit (Invitrogen). Real-time PCR was performed using SYBRH Select Master Mix for CFX (Invitrogen). Relative quantification was achieved by normalization to the amount of GAPDH control RNA. The primers used are shown in Table 1.
Chromatin immunoprecipitation assay
Cultured MDA-MB-231-VECT and MDA-MB-231-SOX4 cells were treated with 1% formaldehyde at 37 °C for 15 min, and lysed with nuclei-swelling buffer. After sonication and centrifugation, cytoplasmic extract was incubated at 4 °C overnight with 5 mg of anti-SOX4 or nonspecific IgG control antibody. Cytoplasmic extract not incubated with antibody was saved as an input sample. The antibody-bound complex was precipitated by protein A-Sepharose beads (Amersham Biosciences, Little Chalfont, Buckinghamshire, UK). The beads were washed and the protein-DNA complex was eluted from the beads with 250 ml of elution buffer (1% SDS and 0.1 M NaHCO3) at 37 °C for 15 min. The DNA in the immunoprecipitated complex and the DNA in the previously saved input fraction were released by incubation at 65 ℃ for 2 h with 200 nM NaCl and 20 mg of proteinase K. DNA was amplified by PCR under the following conditions: 96 °C for 15 s, 54 °C for 30 s and 72 °C for 30 s, and 40 cycles. The primers used are showed in Table 2.
Immunohistochemistry (IHC)
Tissue chip slides (ZL-BRM961, SUPERBIOTEK, Shanghai, China), which contained primary breast cancers each paired with a metastatic tumor in a lymph node (n=36), were deparaffinized in xylene and rehydrated in graded alcohol solution, followed by treatment with 3% H2O2 to quench the endogenous peroxidase for 15 min and 1% BSA for 1 h at room temperature to block the potential nonspecific binding. The slides were then incubated with primary monoclonal antibody against SOX4 (Cat# GR264610-1, Abcam, Cambridge, UK) or CXCR7 (Cat#GR245543-1, Abcam) overnight at 4 °C prior to incubation with biotinylated secondary antibody for 20 min at room temperature. Finally, the slides were treated with avidin-biotin complex reagent and stained with 3, 3 -diaminobenzidine according to manufacturer's protocol. Staining results were analyzed for the staining intensity as well as the percentage of positive cells. The staining intensity was scored 0 point for no obvious coloring, 1 point for mild, 2 points for moderate, or 3 points for strong. The percentage of positive cells for each slide was calculated from 3 different microscopic fields (200x) and was scored as follows: 0 to 5 %, 0 point; 6 % to 25 %, 1 point; 26 % to 50 %, 2 points; 51 % to 75%, 3 points; and> 75%, 4 points. The overall score was the sum of the staining intensity and the percentage of positive cells: 0, negative; 2 to 3, weakly positive; 4 to 5, moderate; and 6 to 7, strongly positive.
Tumor xenograft
Six-week-old male mice with severe combined immunodeficiency (SCID) were obtained from Jackson Laboratory (Bar Harbor, ME, USA). Cells (5 x 106) expressing luciferase were injected into the left mammary fat pad of each mouse. The tumors were examined weekly using bioluminescent imaging after intraperitoneal injection of 150 mg/kg D-luciferin (Caliper LifeSciences, Hopkinton, MA, USA). The length (a) and width (b) of the tumors were also recorded every week. The tumor volume was calculated by the formula of V = ab2/2 mm3. In the study of metastasis, tumors were removed when their sizes exceeded 2 cm x 2 cm. Metastasis was followed by bioluminescent imaging. By the end of the 16th week, mice were euthanized, dissected and examined for organ metastases. In the study of resistance to paclitaxel, 3 weeks after cell injection, i.e., day 0 of treatment, the tumor-bearing mice were administered with paclitaxel at a dose of 10 mg/kg or the same volume of phosphate buffered saline (PBS). The treatment was repeated at day 7 and the tumors were examined using bioluminescent imaging at day 14.