Experimental human tissues and animals
The research tissues of CRC patients and HC people were obtained from The Affiliated Cancer Hospital of Nanjing Medical University and all the patients signed the written consents. Tissue debris was immediately frozen in liquid nitrogen after surgery and stored at − 80 °C. All animal experiments were designed according to the standards of the Guide for the Care and Use of Laboratory Animals (NIH, 8th edition, 2011). The Ethics Committee of The Affiliated Cancer Hospital of Nanjing Medical University approved present research.
Cell culture
Four human CRC cell lines LoVo, HCT116, SW480, SW620 and human intestinal epithelial cells (HIECs) were purchased from American Type Culture Collection (ATCC, USA) and cultured in DMEM (Gibco, USA) contained with 10% fetal bovine serum (FBS; Gibco, USA), 100 IU/mL penicillin and 100 mg/mL streptomycin in humidified atmosphere containing 5% CO2 at 37 °C.
Cell transfection
The shRNA-BCYRN1 (sh-BCYRN1), shRNA-KRAS (sh-KRAS) and corresponding shRNA negative control (sh-NC) transfection were performed using Lipofectamine 3000 reagent (Invitrogen, USA) conforming to the manufacturer’s introductions. Besides, RNAifectin™ transfection reagent, negative control (NC), miR-204-3p mimic and miR-204-3p inhibitor were obtained from Applied Biological Materials Inc. (Richmond, Canada). HIECs and CRC cells were cultured into 6-well plates for transfection, and the efficiency of transfection was determined by qRT-PCR.
RNA extraction and qRT-PCR
Total RNA was exacted from human tissues, mouse tissues and cells with a Trizol reagent (Life Technologies, USA). Reverse transcriptase experimments were performed with PrimeScript® RT reagent Kits (Takara Bio Inc, Japan) and StepOnePlus™ Real-Time PCR System (Applied Biosystems, USA). Next, the quantitative reactions were made with SYBR Green RT-PCR (Takara Biotechnology Co., Japan) by StepOnePlus™ system. GAPDH and U6 snRNA were used as the internal control, respectively. Primers were used for qPCR as follows: BCYRN1 sense: TAAGCTTGTAACCTGCACCCGATTCACAG; anti-sense: TGGCAGCATACTCCTGACCATACTACCCG; miR-204-3p sense: GGGAAGGCAAAGGGACGT; anti-sense: CTCAACTGGTGTCGTGGATGC; KRAS sense: AGGCCTGCTGAAAATGACTGAATAT; anti-sense: GCTGTATCGTCAAGGCACTCTT; GAPDH sense: 5’-GGAAAGCTGTGGCGTGAT-3’, anti-sense: 5’- AAGGTGGAAGAATGGGAGTT-3’; U6 sense: CTCGCTTCGGCAGCACAT; anti-sense: AACGCTTCACGAATTTGCGT.
Evaluation of cell proliferation
Cell proliferation was detected by cell counting kit-8 (CCK-8) report, 5-ethynyl-2’-deoxyuridine (EdU) incorporation test, a nucleoprotein Ki-67 and proliferating cell nuclear antigen (PCNA) expression. Firstly, for CCK-8 experiment, cells were seeded into a 96-well plate with 10% FBS DMEM for 24 h. Then, the medium was changed with serum free DMEM for CCK-8 kit (Beyotime Biotechnology, China) detection. The microplate reader (ELX800, USA) was used to determine the absorbance at 450 nm, which is reflecting cell viability and proliferation. Secondly, cells were seeded into a 24-well plate for EdU assessment. After 48-h transfection, DNA synthesis was examined with EdU incorporation assay (RiboBio, China). The proportion of EdU-positive cells was analyzed by a fluorescence microscopy (Axio Vert. A1, Germany). Lastly, cell proliferation was evaluated by Ki-67 and PCNA expression. Ki-67 is a nucleoprotein that is a marker of tumor proliferation [28]. PCNA acts on chromatin and is participated in all aspects of the DNA replication chain [25]. The expression levels of Ki-67 and PCNA can evaluate the status of cell proliferation.
Evaluation of cell migration and invasion
Cell migration and invasion were assessed with the Wound-Healing assay, Transwell assay and invasion-related proteins expression. For Wound-Healing assay, cells were seeded into a 6-well plate. A sterile 1 mL pipette tip was used to scratch the bottom of plate to form a gap. The images of cell migration were captured at 0 h and 24 h after transfection, respectively, with an inverted microscope (Axio Vert. A1, Germany). The average distance of migration was calculated, which reflects the cell migration capacity. For Transwell assay, cells were plated into the no FBS medium in the upper chamber of a 12-well Transwell with 8-µm pore size (Merck kGaA, Germany). 10% FBS medium was added into the lower chamber. After 24 h, the cells that migrated to the submembrane surface were stained with crystal violet. And stained cells were counted in 6 randomly selected regions. In addition, Cyclooxygenase-2 (Cox-2) is an enzyme complex that plays significant roles in metastasis and invasion of malignancies [29]. Matrix metalloproteinase (MMP) family, especially the gelatinases MMP-2 and MMP-9, are recognized as markers of tumor migration and invasion [30]. The expression of Cox-2, MMP-2 and MMP-9 can reflect the status of cell migration and invasion.
Flow cytometric analysis
Flow cytometric analysis was designed to evaluate whether BCYRN1 regulated the apoptosis of CRC cells. Consistently, cells were seeded into a 6-well plate. The cells were collected and stained with Annexin V-FITC (Beyotime Biotechnology, China) and propidium iodide (PI) regent after 48 h transfection according to the manufacturer’s instructions. Then, the cell apoptosis was determined by a flow cytometry (Becton Dickinson, USA).
Dual luciferase reporter assay
The partial sequences of BCYRN1 and 3'-untranslated region (3’-UTR) of KRAS containing the putative binding sites of miR-204-3p were synthesized and inserted into a luciferase reporter vector plasmid (Genepharma, China). According to the instruction, firefly luciferase reporter plasmid, equal amounts of miR-204-3p mimics or negative control mimics (NC) were transfected into cells, respectively. Then, the relative luciferase activities were detected by the Dual-Luciferase Reporter Assay System (Promega, USA) on Luminometer 20/20n (Turmer Biosystems, USA) after transfection for 48 h.
In vivo experiments
The nude mice were injected subcutaneously with CRC cells (about 106 cells) into the right flanks. Then, sh-NC or sh-BCYRN1 was directly injected into the mice to knockdown the BCYRN1. Tumor size was measured every 5 day for total of 6 times. At the end of the experiments, mice were humanely sacrificed with overdose anesthesia for the collection of tumors. Each tumor was weighed to evaluate the effects of BCYRN1 on the development of tumors.
Immunohistochemistry
Tumors were obtained as above description, fixed in 4% paraformaldehyde, embedded in paraffin, and then cut into 10 µm sections. After de-paraffinization and block, the sections incubated with primary anti-Ki67 (1:100; Abcam, USA) overnight at 4 °C. The immunofluorescence images were captured with an Olympus BX51 microscope (Olympus, Japan) after incubating horseradish peroxidase-conjugated goat anti-rabbit antibody.
HE staining and TUNEL fluorescence staining
Hematoxylin-eosin (HE) staining and terminal deoxynucleotidyl transferase (TdT)-mediated dUTP nick-end labeling (TUNEL) staining were performed to detect cancer cell apoptosis of mouse tumor tissues. Briefly, mouse tumor tissues were prefixed, and the paraffin-embedded sections were stained with Hematoxylin-eosin and TUNEL (containing 2 µL TdT enzyme, 48 µL Fluorescent labeling solution and 50 µL TUNEL detection solution) according to the manufacturer’s instructions. The images were obtained with an Olympus BX51 microscope (Olympus, Japan) coupled with an Olympus DP70 digital camera.
Western blot analysis
The protein expression levels of Ki-67, PCNA, Cox-2, MMP-2, MMP-9, Bax, Bcl-2, Cleaved caspase-3, Cleaved caspase-9 and KRAS were detected by Western blot analysis. Total protein was extracted and separated with SDS-PAGE, then, transferred to PVDF membrane. Protein bands were visualized with Enhanced Chemiluminescence Detection Kit (Thermo Fisher Scientific, USA). All primary antibodies were obtained from Abcam (Cambridge, USA).
Statistical analysis
Experiments were conducted in a randomized, double-blinded situation. Data are expressed as mean ± SD. Student’s unpaired t-test was detected to compare the difference between two groups. One-way or two-way ANOVA followed by post hoc Bonferroni test was employed for multiple comparisons. Statistical significance was considered as *P < 0.05, **P < 0.01, and ***P < 0.001.