2.1 Database selection and analysis
Based on the gene expression data in CCA from the The Cancer Genome Atlas(TCGA) database (https://tcga-data.nci.nih.gov/tcga), FPKM data of CCA were downloaded and analyzed for any differences, and the mRNA expression levels of EMI2 were presented using a box diagram. From the GEO database (https://www.ncbi.nlm.nih.gov/geo/) to download GSE32225 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE32225), and GSE22633 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22633) data processing, and differential genes were screened by limMA package. The TIMER (http://timer.cistrome.org/) was used to check the quantity of EMI2 expressed in various tumors.
PROMO (http://alggen.lsi.upc.es/cgi-bin/promo_v3/promo/promoinit.cgi?dirDB=TF_8.3) and ChIPBase databases (http://rna.sysu.edu.cn/chipbase/) were used to predict the transcription factors of EMI2, then take intersection with Wayne figure, YY1 and STAT4 were found to be mating sites. JASPAR database (http://www.jaspar.genereg.net) was used to predict the possible binding sites of EMI2 and YY1.
2.2 Tissue sample collection
Paired tumor and paracancerous tissue samples were collected from 8 patients with CCA who underwent surgical resection in the First Affiliated Hospital of the Bengbu Medical College from January 2020 to January 2021. The tissue samples were cryopreserved at -80°C. All patients signed informed consent, and the study was approved by the Ethics Committee of the First Affiliated Hospital of the Bengbu Medical College.
2.3 Cell culture and transfection
CCA cell lines (RBE, HuCCT1, HUCC-9810, and QBC-939) were purchased from the Shanghai Cell Bank, Chinese Academy of Sciences, and normal bile duct epithelial cell line (HIBEpiC) was purchased from the Shanghai Tongpei Biotechnology Co., Ltd. HuCCT1, RBE, HUCC-9810, QBC-939, and HIBEpiC cells were treated with RPMI-1640 medium (Gibco, USA), 10% fetal bovine serum (FBS, Gibco, USA), and 1% penicillin-streptomycin (Biosharp, China) and incubated at 37.5°C with 5% CO2.
To construct a stable transgenic vector using human EMI2 lentivirus, the single-stranded DNA oligonucleotide was synthesized by RNA interference target sequence technique, and the double-stranded DNA was annealed to form the double-stranded DNA. The double-stranded DNA was inserted into the PLENR-GPH vector of RNAi lentivirus after digestion using multiple restriction enzymes. The interference sequence was 5'-GCGTGAAATTGTTGTTCAAGA-3' and the control sequence was 5'-TTCTCCGAACGTGTCACGT-3' (Shanghai Baioujing Biotechnology Co., Ltd.). The interference sequence of YY1 was 5’-CCAAACAACUGGCAGAAUUTT-3’ (Shanghai Baioujing Biotechnology Co., Ltd.). The ligation products were then used to transform competent Escherichia coli cells, and the recombinants were detected using PCR. Lentiviral vectors were collected 72 h after transfection. Subsequently, the recombinant lentivirus (100 µL, 1 × 107 units/mL) with green fluorescent protein were cultured at a density of 2 × 105 cells/well for 24 h. After 72 hours, stable lentiviral strains expressing shCtrl and shEMI2 were obtained. Meanwhile, plasmids oeEMI2, oeYY1, and oeCtrl were constructed (Shanghai Baioujing Biotechnology Co., Ltd.).
2.4 RNA extraction and RT-PCR
Total RNA was extracted with Trizol reagent (Invitrogen, USA), and then reverse transcription was performed using the cDNA preparation kit according to the manufacturer’s instructions (Thermo, USA,). The primers for EMI2, YY1, and their internal reference sequences were designed using Primer 5.0 (Table S1). Then, quantitative PCR was performed using a real-time PCR machine (MX3000p, Agilent).
2.5 Western blotting
The transfected and control cells were digested using RIPA lysis buffer with a protease inhibitor and the total proteins were extracted. BCA kit (Beyotime Biotechnology, China) was used to detect the protein content. After quantification, the protein samples were subjected to the SDS-PAGE gel electrophoresis separation. Then, the target proteins were transferred to polyvinylidene fluoride (PVDF) membrane, which was sealed with protein-free rapid blocking solution (Beyotime Biotechnology, China) for 30 min. The primary antibody was added and the membranes were incubated at 4°C overnight. Then use PBST to clean the membrane 3 times. They were imaged after incubation with the Tanon HighsigeCl western blotting substrate reagent for 2 h using a Biorad imaging instrument. The blots were analyzed by Image J software.
2.6 CCK8 assay
After digestion and centrifugation, cells from each treatment group were inoculated in 96-well plates at a cell density of 5000/well and incubated. CCK-8 reagent (Beyotime Biotechnology) was added to each well after 1, 2, 3, 4, and 5 d of culture. After adding the CCK-8 reagent, the cells were incubated for 1–2 h at 37°C. The optical density of cells within each group was detected using a microplate analyzer at 450 nm.
2.7 Tissue microarray (TMA) and immunohistochemistry (IHC)
TMA included tissue samples from 75 patients with bile duct carcinoma (48 patients with extrahepatic bile duct adenocarcinoma, 27 patients with intrahepatic bile duct adenocarcinoma) and 5 cases had normal intrahepatic bile duct tissue. The microarray chips were purchased from Shanghai Kejie Biological Technology Co., Ltd. The patients’ age, gender, TNM stage, and clinicopathological grade were noted. After immunohistochemical staining, two pathologists analyzed the results based on the intensity and range of staining using a previously described method[22]. The scores given by the pathologists were 0, no staining; 1, light yellow; 2, brown-yellow; and 3 brown for the standards. Positive cell percentage standards were 0–10%, 0 points; 10–25%, 1 point; 26–50%, 2 points; 51–75%, 3 points; and 76–100%, 4 points. The final result was calculated as the number of positive cells multiplied by the staining intensity.
2.8 Cell cloning
The cells from each treatment group were inoculated in 6-well plates with an inoculation density of 1000 cells/well and a medium containing 10% FBS was added. The cultures were terminated after 2 w. After removing the supernatant, the cells were washed with PBS thrice and 4% paraformaldehyde was added for 15 min for fixing the cells. The cells were then washed with PBS twice. After staining with crystal violet for 15 min, the cells were washed with PBS twice.
2.9 Transwell and wound-healing assays
Migration assay: Cells from each treatment group were inoculated in a transwell chamber containing a serum-free medium separately at a density of 1 × 104 cells/well. After 24 h, the supernatant was removed, the cells were washed with PBS thrice, fixed with 4% paraformaldehyde, stained with crystal violet, and imaged. Six visual felds/holes were randomly selected and cells were counted for subsequent analysis.
Invasion assay: Firstly, 40ul matrix glue (diluted in 1:8 medium) was added to the upper chamber of Transwell chamber and fixed in an incubator at 37°C for 1h. The cells from each treatment group were inoculated in a serum-free medium separately with a density of 1 × 104 cells/well. Then culture for 48h, fixed with 4% paraformaldehyde, and stained with crystal violet. Six visual felds were selected to photograph and count the cells of each group.
Wound-healing assay: Cells from each treatment group were inoculated in 6-well plates. When the cell density was about 80%, scars were made with 200-ul spears, added 2ml/ well medium containing 2% fetal bovine serum, and photographed at 0, 24, and 48 h.
2.10 Luciferase reporter assay
The binding sites of EMI2 and YY1 were predicted using JAPAR data, and the first three significant hits were selected to construct the plasmids. All vectors were verified by sequencing them. The constructed plasmid was transfected into 293T cells in 96-well plates. After transfection for 48 h, the medium was removed and the cells were washed once with PBS. After adding the lysate, pre-mixed LAR II was added and the 96-well plates were placed on a shaker at room temperature for 15 min. Then luciferase activity was detected.
2.11 Cell cycle and apoptosis assays
The cells from each treatment group were inoculated in 6-well plates with a density of 30 × 104 cells/well. After 24 h of culture, the cells were digested using trypsin (without EDTA). The cells were centrifuged at 1000 rpm for 10 min, collected, and washed with PBS twice. The centrifugation was continued for 10 min (at 1000 rpm), and the reagents from the APC single-dye apoptosis kit (Beyotime Biotechnology) were added successively according to the manufacturer’s instructions. The samples were tested by flow cytometry. After digestion and centrifugation, the cells from the different treatment groups were fixed with 70% ethanol at 4°C for 12 h. Then the cells were washed with PBS once. After centrifugation, reagents from the cell cycle kit (Beyotime Biotechnology) were successively added according to the manufacturer’s instructions.
2.12 Animals
Four-week-old BALB/c female nude mice were purchased from Shanghai Lingchang Biotechnology Co., Ltd. The ethics approval to perform the animal experiments was obtained from the Bengbu Medical College. The QBC939 cells of stable transfected strains shEMI2/shCTRL were injected 1 cm into the armpit of the mice. Three weeks after the injection, the mice were sacrificed by neck removal under anesthesia, and the tumors were removed. The tumors were embedded in paraffin and immunohistochemical analysis was performed.
2.13 Data statistics
Statistical analyses were performed using Prism 8.0 (GraphPad Software). Data are expressed as mean ± standard deviation (x ± s), and the differences between groups were analyzed using independent t-tests or one-way analyses of variance. P < 0.05 was considered statistically significant. Bioinformatic analysis was performed using R software (version 4.0). All experiments were repeated three times.