Cell Culture and Reagents
Human pancreatic cancer cell lines, including PANC-1, SW1990, CFPAC-1, BxPC-3, HPAC, MIAPaCa-2, and Capan-1, were purchased from the American Type Culture Collection (Manassas, VA, USA) and maintained in DMEM (Gibco, Grand Island, NY, USA) supplemented with 10 % fetal bovine serum (FBS), 100 units/ml penicillin, and 100 mg/ml streptomycin (Gibco). The cultures were incubated at 37 °C in a humidified atmosphere with 5 % CO2. Cells were passaged every 2–3 days to support exponential growth. SATB1, MMP2, MMP9, MYC and β-actin antibodies, SATB1 siRNA, and MYC siRNA were purchased from Santa Cruz Biotechnology (Santa Cruz, CA, USA). Horseradish peroxidase (HRP)-conjugated mouse and goat secondary antibodies were purchased from Genscript (Nanjing, China).
Specimen Collection and Ethics Statement
Sixteen pairs of human primary pancreatic carcinomas and adjacent normal pancreatic tissue samples and 68 formalin-fixed paraffin-embedded pancreatic cancer tissue samples were surgically removed and snap-frozen in liquid nitrogen or fixed in 10 % formalin and embedded in paraffin; these tissues samples were obtained from fresh pancreaticoduodenectomy (Whipple resection) or from the body and tail of pancreas resections, along with pathology summaries at the Department of General Surgery of the First Affiliated Hospital of Nanjing Medical University between 2006 and 2009. Pancreatic cancer staging was followed the guideline as we described before [34]. All human tissue samples were obtained according to the ethical guidelines of the Declaration of Helsinki. This study was approved by Ethics Committee of Nanjing Medical University. All patients participated after having provided informed consent. Tumor stage was evaluated in accordance with the tumor-node metastasis (TNM) classification system UICC/AJCC 2002.
SATB1 Knockdown or Overexpression and MYC Knockdown
SATB1 shRNA was designed based on the SATB1 mRNA sequence [GenBank: NM_002971] with BLOCK-iT™ RNAi Designer (Invitrogen Life Technologies, Carlsbad, CA, USA): SATB1-shRNA oligoduplexes (5′-GGATTTGGAAGAGAGTGTC-3′) were synthesized and cloned into pGCsi-H1/Neo/GFP (Genechem, Shanghai, China). Pancreatic cancer cell line SW1990, which expresses high level of endogenous SATB1, was transfected with pGCsi-H1/Neo/GFP-SATB1-shRNA or empty vector using Lipofectamine 2000 (Invitrogen Life Technologies) following the manufacturer’s instruction. Forty-eight hours later, the transfected cells were selected and maintained in media containing 800 μg/ml G418 (Invitrogen Life Technologies). The full-length SATB1 coding sequence (CDS) was cloned into pcDNA3.1 mammalian expression construct (Invitrogen Life Technologies) defining as pcDNA3.1-SATB1. Pancreatic cancer cell line PANC-1 expressing low level of endogenous SATB1 was transfected with pcDNA3.1-SATB1 or empty vector using Lipofectamine 2000 (Invitrogen Life Technologies) following the manufacturer’s instruction. PANC-1 cells stably expressing SATB1 or empty vector was selected and maintained in media containing 600 μg/ml G418. SATB1 siRNA was transfected using RNAifectin™ transfection reagent (Applied Biological Materials Inc, Richmond, BC, Canada) in SW1990 or Capan-1 cells with relative high levels of SATB1 following manufacturer’s protocol. MYC siRNA was transfected with RNAifectin™ transfection reagent (Applied Biological Materials Inc) in PANC-1 cells that stably overexpressing SATB1 and in control cells following the manufacturer’s protocol to knock down MYC.
Cell Growth Curves
Cellular growth was evaluated by MTT assays. SW1990 stably knockdown, PANC-1 stably overexpressing SATB1, or control cells were seeded at a density of 1.0 × 103 cells/well in 96-well plates. After cells were allowed to adhere for 2 h, and at every 12 h until 96 h, MTT (Sigma-Aldrich, St. Louis, MO, USA) was added to each well at a final concentration of 0.5 mg/ml, followed by incubation at 37 °C for 4 h. The medium was then removed, and 200 μl of DMSO was added to each well. The absorbance of the mixture was measured at 490 nm using a microplate ELISA reader (Bio-Rad Laboratories, Hercules, CA, USA). The relative cell number was calculated using the following equation: relative cell number = mean experimental absorbance/mean 2-h absorbance.
Cell Cycle Analysis
SW1990 stably expressing SATB1 shRNA or empty vector cells were incubated in six-well plates (5 × 104 cells/well). Forty-eight hours later, cells were fixed with 80 % chilled ethanol and then incubated with 0.5 % Triton X-100 solution containing 1 mg/ml RNase A (Qiagen, Germantown, MD, USA) at 37 °C for 30 min. Propidium iodide (PI) (Sigma) was added to each well at a final concentration of 50 μg/ml later, followed by a 30-min incubation in the dark. Cellular DNA content was analyzed using a FACS machine (Becton–Dickinson, Franklin Lakes, NJ, USA). Data were processed using WinMDI29 software (Becton–Dickinson).
Cell Migration and Invasion Assays
Cell migration and invasion assays were performed using 24-well transwell plates (8-μm pore size) from Sigma. In the invasion assays, Matrigel (BD Biosciences, Morrisville, NC, USA) was diluted to 1 mg/ml in serum-free, cold DMEM, and 100 μl of the diluted Matrigel was added to each insert chamber. The plates were incubated at 37 °C for 4 h to allow gelling. SW1990 stably knockdown, PANC-1 stably overexpressing SATB1, or control cells were harvested from culture plates and re-suspended in serum-free culture medium at a density of 105 cells/ml. After collecting the cell samples, 100 μl of the cell suspension was added into each insert chamber. The lower chamber was filled with 600 μl of culture media containing 10 % FBS. After 24 h of incubation, non-invading cells on the top of the membrane were removed using cotton swabs. Invaded cells on the bottom of the membrane were fixed with 4 % paraformaldehyde for 15 min, followed by staining with 0.05 % crystal violet for 2 h. Photographs were taken, and all the cells on the entire membrane were counted. The relative invasion activity was calculated after normalization to cell migration.
RT-PCR and Quantitative Real-Time PCR
Total RNA was extracted from cancer cell lines using Trizol reagent (Invitrogen Life Technologies). Total RNA (1 μg) was reverse-transcribed by A3500 AMV RT-PCR (reverse transcription polymerase chain reaction) system (Promega, Madison, WI, USA). The products of the PCR were electrophoresed on 1 % agarose gels, visualized by ethidium bromide staining and quantified using Quantity One software (Bio-Rad, Hercules, CA, USA). The results were analyzed using SDS 2.3 software (Invitrogen Life Technologies). β-Actin was used as the internal positive control and reference gene for the normalization of PCR cycle numbers to ensure a linear amplification of templates in each experiment. The quantitative real-time PCR was performed and analyzed in a 7900HT (Invitrogen Life Technologies) using SYBR Green Real-time PCR Master Mix (TOYOBO, Shanghai, China).
Western Blotting
Total protein was extracted using a lysis buffer containing 50 mM Tris–HCl (pH 7.4), 150 mM NaCl, 1 % Triton X-100, 0.1 % SDS, and 1 mM EDTA supplemented with protease inhibitors and phosphatase inhibitors provided by Sigma. The protein extract was loaded, size-fractionated by SDS–polyacrylamide gel electrophoresis, and transferred to PVDF membranes (Bio-Rad). After blocking, the membranes were incubated with primary antibodies at 4 °C overnight. Membranes were probed with specific antibodies, and proteins were visualized by using HRP-conjugated secondary antibodies and Immobilon Western Chemiluminescent HRP Substrate Detection Reagent (Millipore, Billerica, MA, USA). Gel loading was normalized for equal β-actin.
EdU Cell Proliferation Assay
Cell proliferation was evaluated using the ClickiT® EdU (5-ethynyl-2′-deoxyuridine) assay (Invitrogen Life Technologies), which measures actively proliferating cells. EdU is incorporated as thymidine analog in the DNA of newly dividing cells and is detected by a copper-catalyzed reaction with Alexa Fluor 594 dye (red fluorescence). SW1990 stably knockdown, PANC-1 stably overexpressing SATB1, or control cells (1.5 × 104) were cultured in 8-well culture slides for 48 h. EdU labeling was done by incubating cells with 10 μM EdU solution prepared in pre-warmed complete medium at 37 °C in an atmosphere containing 5 % CO2 for 1 h. Next, cells were fixed in 3.7 % paraformaldehyde solution prepared in 1× PBS for 15 min at room temperature followed by two washes with 3 % BSA in PBS. Then, cells were permeabilized by treating with permeabilization buffer (0.5 % Triton X-100 in PBS) for 20 min. After rinsing the cells with wash solution, cells were incubated with 1× ClickiT® reaction cocktail containing ClickiT® reaction buffer, CuSO4 solution, 1× ClickiT® reaction buffer additive, and Alexa Fluor 594 dye for 30 min at room temperature in a dark humidified chamber. Before visualizing under a fluorescence microscope (Olympus Co., Tokyo, Japan) at 40× magnification, cells were washed twice with 3 % BSA in PBS and the nuclei are counterstained with blue fluorescent Hoechst 33342. All experiments were performed in triplicate, and 500 cells were counted from each experiment. The percentage of cells with nuclear EdU staining was calculated and graphed.
Evaluation of Immunohistochemical Staining and Scoring
Patterns of staining, staining intensities, and percentages of SATB1-expressing cells in 68 pancreatic cancer tissue samples were recorded. The staining patterns were evaluated using the immunoreactive score (IRS) recommended by Stegner [35]. In this scoring system, IRS = SI (staining intensity) × PP (percentage of positive cells). SI was defined as 0, negative; 1, weak; 2, moderate; and 3, strong. PP was determined as 1, 0–9 % positive cells; 2, 10–50 % positive cells; and 3, >50 % positive cells. One hundred cells were counted in each of ten 40× visual fields from different areas of each random section chosen for IRS evaluation. Then, the average IRS was calculated for each sample. The intensity of SATB1 staining was defined as “negative” or “positive,” corresponding to IRS values below 1 or above 1, respectively. Sample sections were reviewed and scored by two researchers including one pathologist.
Dual-Luciferase Reporter Assay
Thirteen different lengths of MYC 5′ promoter regions (−3090 to +100) were cloned into pGL3 luciferase reporter vector (Promega, Madison, WI, USA) and defined as pGL3-R1 to R13. SW1990 stably knockdown SATB1 or control cells in 24-well plates were transfected with 100 ng of pGL3-R1 to R13 and 50 ng of normalization plasmid pRL-TK Renilla. The dual-luciferase reporter assay was performed 48 h after transfection using a luciferase assay system (Promega). Activities were normalized to pRL-TK activity and further normalized to pGL3-basic group.
Statistical Analyses
Each experiment was performed at least in triplicate. PCR results were analyzed using Quality One software (BIO-RAD). Statistical analyses were performed using SPSS 13.0. MTT, migration/invasion, EdU, promoter reporter, qRT-PCR assays, and growth curve analysis in cells were assessed using the two-tailed Student’s t test, Mann–Whitney U test, or one-way ANOVA. The Chi-squared test was used to compare categorical groups. A P value less than 0.05 was considered significant.