Clinical specimen and cell lines
Human primary CRC and adjacent tissues were extracted from 36 patients who underwent surgical resections from the First Affiliated Hospital of Dalian Medical University. All tumor tissues were confirmed by histological examination as adenocarcinoma of the colorectal. Tissues were stored in liquid nitrogen for Quantitative Real-Time PCR (QRT-PCR) and immunohistochemistry experiments. The research protocol was approved by the Ethics Committee of the First Affiliated Hospital of Dalian Medical University (YJ-KY-FB-2016-16). CRC cell lines HCT-8, Caco2, SW480,SW620, LOVO and human normal colorectal epithelial cell line (FHC) were obtained from KeyGEN Company (Nanjing, Jiangsu, China) and maintained as previously described[21].
Cell transfection
The ampliations of LEF1-AS1 and FUT8 were clone into the expression vector pcDNA3.1 (Invitrogen). Small interfering RNA of LEF1-AS1, LEF1 and FUT8, scramble siRNA (siSCR), short hairpin RNA for LEF1-AS1 and scramble shRNA were synthesized by GenePharma. Lipofectamine 3000 Reagents (Invitrogen Co., Carlsbad, CA, USA) were used for cell transfection. QRT-PCR was used to assess the transfection efficiency.
RNA isolation and qRT-PCR
Total RNA extraction, from the clinical tissues and cell lines was accomplished by TRIzol reagent (Invitrogen, Carlsbad, CA, USA), and using the QuantiTect Reverse Transcription Kit (QIAGEN, valencia, CA, USA) for cDNA synthesized according to the manufacturer’s protocol. RT-PCR analyses were performed on LightCycler 96 detection system (Roche) according to the manufacturer's instructions. All mRNA expression levels were normalized to GAPDH. Relative fold differences were determined using the method of delta–delta CT.
Western blot analysis
Cells were washed with phosphate-buffered saline (PBS) and dissolved in a lysis buffer containing a mixture of protease inhibitors, and the total protein was obtained. Proteins were electrophoresed with 10% SDS-PAGE gels and transferred to the polyvinylidene difluoride membranes (Millipore, Bedford, MA, USA). Primary antibodies were incubated at 4°C overnight. Membrane proteins were incubated with anti-rabbit IgG at 37 °C. Immunodetection was acquired with the ECL Western blotting kit. All bands were analyzed by LabWorks (TM ver4.6, UVP, BioImaging Systems, NY, USA).
Lectin blot analysis
The CRC cells were lysed and separated via 10% SDS-PAGE and transferred to polyvinylidene difluoride (PVDF) membranes (Millipore, Bedford, MA, USA). Then the PVDF membranes were incubated with the biotinylated Lens Culinaris Agglutinin (LCA) (Vector Laboratories, Burlingame, CA, USA) for 1h at room temperature. The membranes were subsequently incubated with horseradish peroxidase streptavidin (Vector Laboratories) for 30 min and detected with an ECL Western blot kit.
Cell growth curve
To assess proliferation, cells were grown for 48 hours (h) under various experimental conditions and proliferation was determined by using the Cell Counting Kit-8 (CCK-8) assay according to the manufacturer’s instructions. 1×103 /well density cells were seeded in 96-well plates and then cultured for 0, 24, 48, 72 h. At these different stages, CCK-8 reagent was added to each well. The optical density (OD) at 450 nm was read in a microplate reader. (Bio-Rad, Hercules, CA, USA)
Colony formation assays
Cells were plated in six well plates at 1.5×103 per well. The medium was renewed at regular intervals. After incubated for 12 days, the colonies were fixed by 4% paraformaldehyde for 20 min, and stained with 0.2% crystal violet. Colonies were photographed and analyzed.
5-Ethynyl-20-deoxyuridine (EDU) incorporation assays
The EDU assay was performed with a KFluor488 EDU Kit (KeyGEN BioTECH, Nanjing, China). Equal number cells were inoculated in 96-well plate overnight. After treated with 50 μM EDU for 2 h at 37 °C, the cells were fixed with 10% formaldehyde, and stained with Click-iT reaction mixture and Hoechst 33342. Images were captured with microscope.
Invision and wound healing assays
Boyden transwell chambers (Corning, New York, USA) were used to detect cell invasive ability in vitro. Invasion assay was performed as described previously[21]. The number of invaded cells on each membrance was counted from 5 random fields using an inverted microscope (20×10).
Cell migration potential was evaluated by measuring the movement of cells that was prepared as described previously[21]. Wound closure was photographed at 0 and 24h after wounding. The migration capability was quantified by the relative gap distance. The experimental results were analyzed with the software ipp6.0.
Flow cytometry analysis
CRC cells with corresponding treatment were collected (5×105). After incubation with 5% BSA, the cells were incubated with FITC-LCA (Vector Laboratories Inc., Burlingame, CA, USA) for 60 min. CRC cells were resuspended in PBS. The FITC fluorescence intensity was immediately detected by FACS Calibur (Becton-Dickinson, CA, USA).
RNA immunoprecipitation (RIP) assay
RIP assay was performed using the Magna RIP™ RNA Binding Protein Immunoprecipitation Kit (Millipore, Bedford, MA, USA). CRC cells were collected and lysed in RIP lysis buffer containing a protease inhibitor cocktail and RNase inhibitor. The cell extracts were incubated with RIP buffer containing magnetic beads conjugated with human anti-Ago2 anti-body (Millipore) or negative control IgG overnight at 4°C. The protein was digested with proteinase K, total RNAs was isolated from the extracts using the TRIzol reagent subsequently. Purified RNA was analyzed by qRT-PCR.
Chromatin Immunoprecipitation (ChIP)
ChIP assays were performed using the ChIP chromatin immunoprecipitation kit (Beyotime, Shanghai, China). Immunoselections of cross-linked protein-DNA were performed using MLL1 or anti-H3K4me3 antibody or rabbit non-immune IgG (as negative control) overnight at 4°C. The precipitated DNAs were analyzed by PCR.
Electrophoretic Mobility Shift Assay (EMSA)
EMSA was performed according to the manufacturer’s instructions. The biotin 3’ end DNA labeling kit and the LightShift chemiluminescent EMSA kit from Pierce Biotechnology were used in the test. DNA probe for EMSA was synthesized as oligonucleotides (the sequence: ATTAACTTTGATCTAGC). In brief, nuclear extracts were isolated from cells and performed with immunoprecipitation by LEF-1 antibody (abcam, UK). The protein extracts were incubated biotin-labeled probes for 20 mins. Then bound DNA complexes were separated on a 5% nondenaturing polyacrylamide gel electrophoresis and transferred to a nylon membrane (Roche). Finally, Biotin-labeled DNA–protein complexes were detected by the streptavidin conjugated with HRP.
Luciferase reporter assay
The pGL3‐LEF1 promoter reporters were cotransfected into SW480 and SW620 cells with siSCR or siLEF1‐AS1. After 48 hours, the luciferase activity of pGL3‐LEF1 promoter was tested by the Luciferase reporter assay system. TOP‐Flash and FOP‐Flash reporters were cotransfected into SW480 and SW620 cells with siSCR or siLEF1‐AS1. At 48 h after transfection, cells were harvested and the relative activities of luciferase were monitored by means of luciferase reporter assay system.
Immunofluorescence staining
Cells were fixed with 4% paraformaldehyde for 20 min and then permeabilized with 0.2%Triton X-100 for 5 min. After permeabilization, cells were incubated with 5% BSA for 30 min and incubated with primary antibodies overnight at 4°C. Cells were incubated with secondary antibody for 1h and then incubated with 4,6-diamino-2-phenylindole (DAPI, Solarbio, Beijing, China) for 5 min. Images were obtained using a fluorescence microscope.
Immunohistochemistry(IHC) staining
The tissue samples were collected and embedded with paraffin. A 5μm thick slice was cut and then tissue slices were deparaffinized, rehydrated, and immersed in 3% hydrogen peroxide for 10 min to block the endogenous peroxidase. The slices were incubated with the corresponding primary antibodies overnight at 4°C. Next day, the secondary streptavidin-horseradish peroxidase-conjugated antibody staining was performed at room temperature, visualized in 3, 3′-diaminobenzidine (DAB) (ZLI9018, ZSGBBIO, China), then counterstained with hematoxylin, dehydrated and cover-slipped.
Animal models
The male nude mice (4-5 weeks old) were purchased from the Model Animal Research Institute of Nanjing University. 2×106 CRC cells in 0.2 ml PBS were subcutaneously injected into the right armpit region of 25 male BALB/c nude mice which were randomly divided into five groups (n=5 for each group). After the seventh day, the tumor size was measured every 5 days with a caliper. Twenty-seven days after the injection, the mice were sacrificed and the tumors were collected and measured.
For the liver metastasis model, the spleen was exposed and injected with 2×106 CRC cells slowly, this procession sustained at least 5 min. Carefully sutured the wound and kept the nude mouse warm and in a sterile environment after surgery. After 6 weeks, the mice were sacrificed, and their spleens and livers were dissected out and removed for IVIS (Carestream Health, Inc.). The lung metastasis model was established by injecting 2×106 CRC cells into the tail vein. After 4 weeks, the mice were sacrificed, tumor in lung metastasis was removed for IVIS (Carestream Health, Inc.).
Statistical analysis
Each experiment was performed at least in triplicate. Data are presented as means ± SD and were analyzed using SPSS 17.0. Student’s t-test was used to compare the means of two groups. The significance of the differences in multiple comparisons was determined using the one-way analysis of variance (ANOVA). Spearman’s correlation analysis was used to assess the association of mRNA expression. P < 0.05 was considered statistically significant.