Ethics statement
This study was conducted in accordance with the ethical standards, the Declaration of Helsinki, and national and international guidelines, and was approved by the authors’ institutional review board, which adheres to generally accepted international guidelines for animal experimentation.
circRNA microarray
Five pairs of CRC tumor tissues and the corresponding adjacent noncancerous tissues, were utilized for circRNA microarrays. The specimens were obtained from patients undergoing surgery in the Peking University People’s Hospital in 2014; detailed information is shown in Additional file 1: Table S1.
Patients and samples
160 CRC patients who were diagnosed and underwent surgery in Peking University People’s Hospital between 2014 and 2017 were included in this study. Fresh colorectal tumor tissues and matched normal colorectal mucosa tissues were obtained from all the 160 patients. The specimens were obtained and immediately frozen in liquid nitrogen and stored at −80 °C until RNA or protein extraction.
Cellular fluorescence in situ hybridization
The cells were fixed with 4% paraformaldehyde for 15min, washed with PBS three times for 5min each time,0.5% TritonX-100 was permeabilized at room temperature for 20min, and washed with PBS three times for 3min each time.Add 3% citric acid freshly diluted pepsin and digest at room temperature for 15min, then expose the nucleic acid fragment, rinse with PBS and add 20μl of pre-hybrid solution, then pre-hybridize at 50°C for 2-4 hours.The hsa_circ_0000231 or miR375-specific probe hybridizes at a constant temperature of 50°C.Hybridization was carried out by SSC at 37°C water temperature, biotinylated mouse anti-digoxigenin was added dropwise, and PBS was washed 3 times for 3min each time, and the excess paper was absorbed by the absorbent paper.After adding DAPI staining for 10min, the specimen was subjected to nuclear staining, washed three times with PBS for 3min each time, and the excess paper was absorbed by the absorbent paper. The liquid was sealed with a liquid containing a fluorescent quencher, and the image was observed and collected under a fluorescence microscope.
Base Scope assay
Base Scope assays were performed in accordance with the manufacturer's instructions (Advanced Cell Diagnostics, Newark, CA, USA). Tissues were sectioned at 5-μm thickness, placed onto Super frost Plus slides (Fisher Scientific, Loughborough, UK), and allowed to dry overnight at 25 °C. Sections were then baked at 60 °C for 1 h before deparaffinizing in xylene (twice for 5 min) and ethanol (twice for 2 min) and dried by baking at 60 °C for 2 min. Then, hydrogen peroxide was applied for 10 min at 25 °C, target retrieval was performed for 15 min at 100 °C, and RNAscope ® Protease III was applied at 40 °C for 30 min, samples were rinsed twice in distilled water between treatments. Base Scope probes (Mm-1700024F13Rik, cat#709881) with positive control (Hs-PPIB, cat # 701031) and positive control (DapB, cat # 701011) were then applied and samples were incubated for 2 h at 40 °C in a HybEZ oven and then with reagents AMP0 (30 min at 40 °C), AMP1 (15 min at 40 °C), AMP2 (30 min at 40 °C), AMP3 (30 min at 40 °C), AMP4 (15 min at 40 °C), AMP5 (30 min at 25 °C), and AMP6 (15 min at 25 °C). Slides were rinsed with wash buffer (twice for 2 min) between AMP incubation steps. Finally, slides were treated with Fast Red for 10 min at 25 °C in the dark and counterstained with Gill's hematoxylin, dried for 15 min at 60 °C, and mounted in Catamount permanent mounting medium (Vector Labs, Burlingame, CA, USA).
Cell lines and cell culture
The human CRC cell lines SW480, SW620, HT29, HCT8, LoVo, colo-205, LS174T, HCT116, RKO and NCM460 cells were purchased from the American Type Culture Collection (Manassas, VA, USA) and subcultured and preserved by our lab.The frozen cells were quickly removed from the liquid nitrogen tank, thawed in a 37°C water bath, then inoculated into a disposable cell culture flask (25cm2), fresh 5ml of DMEM medium was added, and then placed in 5% CO2 incubator at 37°C, and the liquid was changed once every 2 days.When the adherent cell fusion degree reached about 90%, the passage was carried out,and then the cells were counted, and then inoculated at a concentration of 1 × 105/mL to continue to be cultured for use.
RNA extraction and quantitative real-time PCR
Total RNA from cell lines and tissue samples was extracted using Trizol (Invitrogen) according to the manufacturer’s instructions. For the plasma, the total RNAs were extracted using mirVanaTM PARISTM microRNA extraction kit (ABI) according to the manufacturer’s instructions. For lncRNA quantification, GAPDH was used as internal control, and PrimeScriptTM RT Master Mix (TAKARA) were used for reverse transcription and real-time PCR. The primer sequences were listed in in Additional file 1: Table S2. All reactions were performed in triplicate. The fold change for each gene relative to the control group was calculated using the 2-ΔΔCt method.
Lentiviral short hairpin (sh)RNA particles
Recombinant lentiviral particles expressing hsa_circ_0000231 or hsa_circ_0000231 small interfering (si)RNA were obtained from GenePharm Co., Ltd. (Shanghai, China). SW480 Cells were grown to approximately 40% confluence and infected with lentiviral particles in complete medium for 48 h. To increase the infection efficiency, cells were co-treated with the cationic polymer polybrene (8g/mL in water). Neither shRNA nor polybrene affected cell viability. siRNA and shRNA had no off-target effects, and did not affect cell adherence, shape, or viability at the indicated multiplicity of infection.
Cell transfection
For in vitro studies, to interfere the expression of hsa_circ_0000231, siRNA interference sequences targeting hsa_circ_0000231 were designed and synthetized (Ribobio, Guangzhou, China), and a final concentration of 50nM were used for transient transfection; to overexpress hsa_circ_0000231, full-length human hsa_circ_0000231 cDNA was cloned into the pcDNA3.1 expression vector (Genechem, Shanghai, China). Lipofectamine 3000 (Invitrogen, Carlsbad, CA, USA) was used for transfection according to manufacturer’s instructions.
For in vivo assays, hsa_circ_0000231 overexpression cell line was used. The hsa_circ_0000231 gene was cloned in to a lentivirus vector LV-GFP-Puro, and SW480 cells were used for infection. Stable transfection cells were established by puromycin antibiotic selection applied for 7 days, with a concentration of 2.5 ug/ml. The hsa_circ_0000231 overexpression cells and control cells were named SW480-LV-hsa_circ_0000231 and SW480-LV-NC, respectively.
Transfection and grouping of cells: Cell transfection was performed in strict accordance with the instructions of Invitrogen's Lipofectamine® 3000 Transfection Reagent: Transfection was performed when the cytoplasm was inoculated with a confluence of about 80%,the Lipofectamine 3000 reagent was diluted with OPTI-MEM culture medium and mixed. Dilute the DNA expression plasmid to be transfected with OPTI-MEM culture medium, then add P3000 reagent and mix well,add diluted DNA expression plasmid in equal volume to each diluted dilution of Lipofectamine 3000 reagent and incubate at room temperature 5min. Add the DNA-liposome mixture to the cell suspension and carefully mix,continue to culture in 5% CO2 incubator at 37°C.
Cell proliferation assay
SW480 and SW620 cells (3 × 103 cells) were seeded in 96-well plates in complete medium and infected with hsa_circ_0000231, hsa_circ_0000231 siRNA. Cell proliferation assay was performed with Cell Counting Kit-8 (CCK8) according to the manufacturer’s protocol, and detected at 0, 24, 48, 72 and 96 h. Cells in each group were tested for 5 replicates. Cell proliferation was evaluated by the cell counting kit-8 method according to the manufacturer’s instructions using a microplate reader (Molecular Devices, Sunnyvale, CA, United States) to measure the absorbance.
For colony formation assay, transfected cells were seeded into each well of a 6-well plate on day 0 then incubated for another 14d. Then, the wells were fixed with 4% paraformaldehyde, and stained with 0.1% crystal violet. The form colonies were counted and analyzed by Image J software.
CCK-8 method for detecting cell proliferation curve
The proliferation of colorectal cancer cells in each group was detected by CCK-8 method. After transfection for 24 hours, the cells were seeded in 96-well plates at 5 × 103cells/well, and 10μl of CCK-8 solution was added to each well. Then, incubate in a 5% CO2 incubator at 37°C.When the cells were grown to the 2d, 3d, 4d, and 5d, the absorbance of the cells at 450nm was measured using an enzyme reader to represent the proliferative activity of the cells during this period. The proliferation curve of each group of cells was plotted, and the difference in cell proliferation rate of each group was compared.
Western blot analysis
Cells were lysed in RIPA buffer, centrifuged at high speed, and then underwent protein quantification using a bicinchoninic acid assay. Cellular proteins were separated by sodium dodecyl sulfate polyacrylamide gel electrophoresis and transferred onto polyvinylidene difluoride membranes. Membranes were incubated with primary antibodies followed by horseradish peroxidase-labeled secondary antibody. GAPDH was used as a loading control. The total protein of CRC cells was exacted with RIPA buffer and separated by 10% SDS-PAGE, then Elec transferred onto a PVDF membrane (Bio-Rad, CA, USA). The membranes were blocked with 5% skimmed milk powder and incubated with primary antibodies against CCND2 (1:1000), IGF2BP3 (1:1000), (Abcam, Burlingame, CA, USA), RB (1:500), and GAPDH (1:5000) (Cell Signaling Technology, Beverly, MA, USA) at 4 °C overnight and then incubated with secondary antibodies (1:5000) (Cell Signaling Technology, Beverly, MA, USA) at room temperature for 2 h. Finally, the bands were examined by Immobilob™ Western Chemiluminescent HRP Substrate (Millipore, Billerica, MA, USA). The antibodies used in the experiments are shown in Additional file 1: Table S3.
Luciferase reporter assay
hsa_circ_0000231 and CCND2 fragments containing two putative wild-type or mutated miR-375-binding sites were amplified by PCR and cloned downstream of the luciferase gene in the pGL3 vector (Promega, Madison, WI, USA). The constructed reporter vectors were verified by sequencing. Luciferase reporter assays were performed by transiently co-transfecting HEK293T cells in 24-well plates with the reporter vectors, miR-216a, and the Rinella luciferase construct using Lipofectamine 2000 (Invitrogen, Waltham, USA). After 48 h transfection, cells were harvested and luciferase activity was measured using the Dual-Luciferase Reporter Assay System (Promega, Madison, WI, USA) and normalized to that of Renilla luciferase.
Biotin-labeled RNA pull-down and mass spectrometry analysis
Biotin-labeled RNA for liner sequence of has_circ_0000231 and CCND2 was generated by an in vitro transcription reaction with the Biotin RNA Labeling Mix (Roche, Mannheim, Germany) and T7 RNA polymerase (Roche, Mannheim, Germany), and then treated with RNase-free DNase I (Takara, Japan). After incubation with guide oligonucleotide targeting circular junction, the liner probe was then circularized using T4 RNA ligase I, treated with RNase R. After purified with RNeasy Mini Kit (Qiagen, Inc., Valencia, CA, USA), the biotin-labeled RNA probe (3μg) was then incubated with cell extracts from CRC cells at room temperature (RT) for 2h, and treated with 35μl of Streptavidin C1 magnetic beads (Invitrogen) for 1 h. after washed, the retrieved protein was detected by western blot or mass spectrometry analysis (CapitalBio Technology, Beijing, China).
RNA immunoprecipitation (RIP)
RIP was conducted with Magna RIP kit (Millipore, Billerica, MA, USA) following manufacturer’s instruments.SW480 cells were harvested 48 h after transfection of miR-375 mimics or miR-NC, and lysed in complete RNA lysis buffer, then cell lysates were incubated with magnetic beads which were conjugated with anti-Argonaute2 (AGO2) (Millipore, Billerica, MA, USA) or negative control IgG antibody (Millipore, Billerica, MA, USA) at 4 °C for 4 h. The beads were washed using washing buffer. Then immunoprecipitated RNA and protein were purified and enriched to detect the targetRNAs and AGO2 by qRT-PCR and western blot.
Nude mouse model of ectopic tumors
Balb/C nude (nu/nu) mice at 6 wk old were purchased from Beijing weitonglihua Experimental Animal Technology Co., Ltd. Tumors were generated by the subcutaneous injection of 2 × 106 SW480 cells infected with hsa_circ_0000231 overexpression cells, or control lentivirus particles and suspended in 50L of PBS into the dorsal region near the thigh. 5 mice were included in each group. Mice were then weighed and assessed for tumor size every 7wk by measuring the tumor length and width.
Statistical Analysis
The data generated in this study were all analyzed by SPSS22.0 statistical software. The measurement data were expressed by mean±standard deviation (x±s). The two groups were compared by T test for statistical analysis. Analysis of variance of factors, count data were analyzed by χ2 test.The survival rates were evaluated by Kaplan-Meier method and tested by log-rank test. The effects of clinical variables on the overall survival of CRC patients were determined by univariate and multivariate Cox proportional hazards regression model. In the multivariate Cox proportional hazards regression model, age, T stage, N stage, clinical stage distant metastasis andtheexpressionofhas_circ_0000231were adjusted for variable analysis. The correlation between groups was analyzed by Pearson correlation,and p<0.05 was used as a criterion for statistically significant differences.