Cell lines, tumor samples, and normal control tissues
Eleven colorectal cell lines (Colo320, DLD-1, HCE8693, HCT-116, HT-29, RKO, SW620, SW480, LOVO, Colo205, and HCT-8) were used. The cell lines were maintained at 37°C in a humidified 5% CO2 incubator in RPMI 1640, Dulbecco’s modified Eagle’s medium, or McCoy’s5A medium (Gibco BRL, Rockville, MD, USA) supplemented with 10% fetal bovine serum (FBS).
Human CRC tissue was collected from patients with adenocarcinoma confirmed pathologically without direct surgical resection of neoadjuvant therapy between December 2000 and April 2007 in Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, and obtained with informed consent from patients.
FOXE1 immunohistochemical analysis was performed on 10 normal colonic mucosa specimens, 128 primary CRC specimens, 27 metastatic lymph node specimens, and 29 colorectal adenomas (including nine tubular adenomas, eight serrated adenomas, and 12 villous adenomas). Methylation-specific PCR (MSP) testing was performed on the tumor tissue and normal adjacent tissue samples of 35 CRC patients stored in a tissue bank. TNM staging for each patient was based on the seventh edition of tumor TNM staging issued by the American Cancer Federation (AJCC, 2010). In terms of the degree of differentiation, we divided tumors into a highly differentiated group (including highly differentiated tubular adenocarcinoma and papillary adenocarcinoma cases), moderately differentiated group (including moderately differentiated tubular adenocarcinoma cases), and poorly differentiated group (including poorly differentiated adenocarcinoma, undifferentiated adenocarcinoma, mucinous adenocarcinoma, and signed-ring cell carcinoma cases).
RNA extraction and semi-quantitative RT-PCR
Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA, USA), as described by the manufacturer. Reverse transcription of the reaction mixture (20 𝜇L) containing total RNA (1 𝜇g) to cDNA was done with M-MLV (Promega Corporation, Madison, WI, USA). The mRNA expression levels of FOXE1 were determined by semi-quantitative reverse-transcription PCR (RT-PCR) with GoTaq polymerase (Promega Corporation, Madison, WI, USA). The transcription of the principal gene GAPDH was used as the internal control. Specific primers were designed according to the FOXE1 sequence. All sequences of primers used were showed in table1.
Bisulfite treatment and promoter methylation analysis
Genome DNA was extracted from tissues using a Tiangen DNA mini kit (Tiangen, Beijing, China), following the manufac turer’s instructions. Bisulfite modification of DNA was performed as previously described [25]. MSP was performed using AmpliTaq-Gold DNA polymerase (Applied Biosystems, Waltham, MA, USA). The PCR products were identified on 1.5% agarose gels.
Demethylation treatment using 5-aza-2′-deoxycytidine and trichostatin A
FOXE1-silenced cell lines were cultured in a 10-cm dish with 1×106 cells each. After overnight culturing, the cells were treated with 5-aza (10 μmol/L) for 72 h and TSA (300 nmol/L) for 24 h. Finally, we harvested the treated cells and extracted DNA and RNA for use.
Immunohistochemistry
IHC was performed using the ChemMate EnVision detection kit (Dako, Carpinteria, CA, USA) as described by the manufacturer. Briefly, the selected sections were incubated with primary FOXE1 antibody (1:250; Abcam), GAPDH antibody (1:200; Invitrogen) overnight at 4 °C, and then incubated with ChemMate EnVision/HRP,rabbit/mouse reagent as a secondary antibody. Afterward, the sections were developed using ChemMate DAB+ chromogen and counterstained with hematoxylin.The percentage of positive cells was evaluated and scored as 0 (< 5%, negative), 1 (5%–25%, sporadic), 2 (26%–50%, local), 3 (51%–75%, diffuse), or 4 (> 75%, positive) points. The intensity of staining was evaluated and scored as 0 (no staining), 1 (weak staining), 2 (moderate staining), or 3 (strong staining) points. Then, both scores were multiplied to produce an immunoreactivity score (IRS) value ranging from 0 to 12 points to evaluate the association of FOXE1 expression with clinicopathological parameters in a manner corresponding to four expression intensities: 0–1 points, negative; 2–4 points, weakly positive (+); 5–8 points, moderately positive (++); and 9–12 points, strongly positive, (+++). Patients were then grouped into two categories based on expression intensity: low expression (negative or weakly positive) and high expression (moderately or strongly positive).
Immunofluorescence
For immunofluorescence, cells (2×105 cells/well) were seeded in the coverslip in a six-well plate with a coverslip inside. After 24 h of culture, cells were fixed in 3.7% paraformaldehyde for 10 min and incubated in PBS with 0.1% Triton X-100 for 4 min on ice, then blocked in 5% FBS for 20 min. Coverslips were moved to a slide and cells were washed three times with PBS; then, we added 200 μL rhodamine phalloidin(Invitrogen, Carlsbad, CA, USA) of 100 nM and additionally incubated cells at room temperature shielded from light for 30 min. Nuclei were stained with PBS with 2 μg/mL of DAPI(Roche, CH) for 10 min. Staining was photographed by an Olympus BX51 microscope (Olympus Corporation, Tokyo, Japan). All of the experiments were repeated three times.
Construction of FOXE1 expression vector
The DLD-1 CRC cell line was transfected with control or FOXE1-expressing plasmid (pCMV6 Entry; Origene, Rockville, MD, USA) using the MegaTran 1.0 transfection reagent (Origene). Stable FOX E1-expressing clones were selected for further study.
Monolayer and soft agar colony formation assays
1000 FOXE1 expression vector stable transfected and parental cells were plated in 10 cm dishes, respectively, and allowed to grow for two weeks at 37°C in 5% CO2. Surviving colonies (≥50 cells/colony) were counted under a microscope after gentian violet staining. The experiments were performed in triplicate.
For the soft agar assay, transfected cells were suspended in a growth medium containing 0.3% agar and seeded into a six-well plate overlaid with 0.5% low-melt agar. Surviving colonies (≥50 cells) were photographed and counted after 14–25 days at 37°C in 5% CO2. The experiments were performed in three wells in triplicate.
Wound-healing assay
Cell motility was assessed using a scratch wound assay. The transfected cells and controls were cultured in six-well dishes until confluent. The cell layers were carefully wounded using sterile tips and washed twice with phosphate-buffered saline. Cells were incubated with fresh medium and photographed under a phase contrast microscope at 0, 12, 24, 36, and 48 h after wounding. The experiments were performed in triplicate.
Cell migration assay
For the Transwell assay, cells were trypsinized and resuspended in a corresponding medium containing 1% FBS at a density of 1×106 cells/mL. One hundred microliters of cell suspension was added to the upper chamber of a Transwell system (Corning, Corning, NY, USA) consisting of inserts containing 8-mm pore-size PET membranes. Six hundred microliters of medium containing 2.5% FBS was placed in the lower chamber. After the indicated amount of incubation time at 37°C in 5% CO2, cells remaining in the upper chamber were removed carefully by cotton swab, and those on the bottom side of the chamber membrane were fixed, stained with 0.25% crystal violet, photographed, and counted under a light microscope. The experiments were performed in triplicate.
In vivo subcutaneous tumor model
All of the in vivo experimental protocols were approved by the animal care committee of Sir Run Run Shaw Hospital, Zhejiang University. Viable FOXE1-transfected cells and controls (5×106 cells in 0.1 mL of PBS) were injected subcutaneously into the right dorsal flank of six-week-old male BALB/c nude mice (six mice per group). Tumor volume was assessed every two days for five weeks. Tumor volume was calculated with the following formula: (short diameter) 2 × (long diameter)/2.
Statistical analysis
Statistical calculations were performed using SPSS version 18.0 for Windows (IBM Corporation, Armonk, NY, USA). Pearson’s chi-squared test was used to analyze the association between FOXE1 expression level and clinicopathological parameters. Results are presented as mean ± standard deviation values, and comparisons between groups were completed by analysis of variance. P < 0.05 was considered statistically significant.