Collection of public HCC database
Differential gene expression profiles in HCC and non-tumor liver tissues were acquired from the Cancer Genome Atlas (TCGA) (http://tcga-data.nci.nih.gov/) [9], and the survival data of HCC patients was also collected and analyzed. LIRIJP (Liver Cancer-RIKEN, JP project) dataset was obtained from the International Cancer Genome Consortium (ICGC) and 18 liver cancer mRNA microarray data sets were acquired from the Gene Expression Omnibus (GEO) databases (http://www.ncbi.nlm.nih.gov/geo). The difference expression between non-tumorous tissues and HCC were identified by the BRB-array tool.
Tissue microarray (TMA)
The TMA was composed of 341 HCC tissues and corresponding adjacent non-tumor tissues (obtained from the 1st Affiliated Hospital of Zhengzhou University between 2011 and 2015), all contained complete clinic-pathological information. This study has been formal approval of the ethics committee in the 1st Affiliated Hospital of Zhengzhou University. All patients signed written informed consent.
Immunohistochemistry (IHC) analysis
Briefly, xylene and graded alcohol were used to deparaffinize and rehydrate the sample sections, respectively. After antigen retrieved and blocking with bovine serum albumin, then the sections were placed at 4℃ temperature with the primary antibodies CBX3 (dilution 1:100, Proteintech Group, Wuhan, China) overnight. Following, the goat anti-rabbit secondary antibodies were added for incubation at normal temperature, and the slides were counterstained with hematoxylin. The NanoZoomer 2.0-RS system was applied to observe the imaging of IHC under Hematoxylin and Eeosin staining. Two experienced pathologists scored the CBX3 staining in an independent and blinded manner. Sections were semi-quantitatively scored for the CBX3 staining patterns as follows: the staining extent in each core was scored as 1+ (< 25% staining of tumor cells), 2+ (25%-50% staining of tumor cells), 3+ (50%-75% staining of tumor cells) or 4+ (> 75% staining of tumor cells. Scores of 3+ and 4+ were defined as exhibiting high expression and scores of 1+ and 2+ were deemed as exhibiting low expression
Cell culture
HCC cell lines (Hep3B and SMMC-7721) and immortalized human normal liver cell lines (L02 and Changliver) were purchased from the Cell Bank of Institutes for Biological Sciences (Shanghai, China). Cells were cultured at stationary 37°C in Dulbecco’s modified Eagle’s medium (Gibco, NY, USA)) with 10% fetal bovine serum in an atmosphere of 5% CO2. All above cell lines in culture had been passaged for less than 6 months when our experiments began.
Polymerase chain reaction (PCR) assays and immunoblotting analysis
Trizol reagent (Invitrogen, Carlsbad, CA, USA) was applied to collect total RNA in accordance with the manufacturer’s instructions. Quantitative reverse transcription-PCR (RT-qPCR) was performed following manufacturer’s protocol. Actin or U6 expression was used to normalize the target genes’ relative expression levels. The 2−ΔΔCt method was used to analyze the data. Every experiment was performed in three times independently.
RIPA protein extraction reagent (KeyGEN, Nanjing, China) was used to extract proteins from the whole cells on ice, Each groove of 12% SDS- PAGE gels was loaded in equivalent proteins, after electrophoresis, proteins were transferred to polyvinylidene difluoride (PVDF) membranes (Millipore, USA). After blocking, the membranes were incubated in 1:1000 anti- CBX3, 1:2000 anti-c-Myc, 1:500 anti-E2F, 1:1000 anti-CCK1, 1:1000 anti-cyclin D1, 1:1000 anti-β-actin for overnight at 4°C. Following, the membranes were placed with goat anti-mouse secondary antibodies (1:1000; Abcam) at normal temperature for two hours. Bands were visualized and analyzed by the Odyssey infrared imaging system and Odyssey 3.0 software (Thermo Scientific), respectively.
Transfection
Three CBX3-target siRNAs (si- CBX3-1, si- CBX3-2 and si- CBX3-3) were utilized to knock down CBX3; a non-silencing siRNA oligonucleotide (si-NC) was a negative control (Invitrogen, CA, USA). CBX3 cDNA was subcloned into a pcDNA3.1 vector as a plasmid (obtained from Invitrogen, CA, USA) to overexpress CBX3, an empty vector was used to be a negative control (pcDNA3.1-NC). MiR-139 mimics, miR-139 inhibitor and the respective negative controls (mimics-NC, inhibitor-NC) and miR-NC were synthesized by GenePharma (Shanghai, China). For transient transfection, HCC cell lines were transfected using Lipofectamine 3000 (Invitrogen, Carlsbad, USA) in line with the manufacturer’s guidelines.
Dual-Luciferase reporter assay
Both wild-type and mutant variant 3’-UTR fragment of CBX3 mRNA were cloned into pmirGLO vectors (Promega, Madison, WI, USA) named as Wt-CBX3 3’-UTR and Mut-CBX3 3’-UTR, respectively. Then Hep3B and SMMC-7721 cells were co-transfected with Wt-CBX3 or Mut-CBX3 vectors and miR-139 mimics or miR-NC with Lipofectamine 3000 reagent (Invitrogen). 48h for transfection later, the Dual-Luciferase Reporter Assay System was used to analyze the luciferase activity (Promega, Madison, USA). The results for experiments are showed as the mean value ± SD in three times.
Cell growth assay
Cell Counting Kit-8 (CCK-8) assay was applied to examine cell growth [10]. Transfected and non-transfected cells were cultured in six 96-well plates. Then the 96-well microplates were put into the incubator. 10ml CCK-8 reagent was added to each well in a 96-well plate every 24 hours for 5 days, after which the plate was incubated for 2 hours at 37°C. Subsequently, the absorbance was record at 450nm by using a spectrophotometer (Molecular Devices, CA, USA).
Colony formation assay was performed to evaluate HCC cell growth. 1,000 cells per well were placed into the 6-well plates. After 14 days for incubation, cells were fixed with paraformaldehyde (4%) and stained with 2% crystal violet, then counted and imaged.
Invasion and wound healing assay
Wound healing assays were utilized to confer the migration ability of HCC cells. Hep3B and SMMC-7721 cells were seeded into the six-well plate, when the growth density reached approximately 90% confluences, we made a gap using a pipette tip of 10 μL. And the gaps were taken photos at 0, 24 and 48 hours later with the microscope (magnification, ×100).
Transwell assay was performed to check the cell invasion ability. 1×104 indicated cells were plated into the transwell insert (the upper chamber) with serum-free medium, DMEM with 10% FBS was filled in the bottom chamber. 24 hours later, the invasive cells on the bottom chamber were fixed and stained. Finally, the migratory cells were imaged and counted.
Bioinformatics analysis
Starbase was used to predict that miR-139 was binding to 3’UTR of CBX3mRNA. Gene set enrichment analysis (GSEA) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were utilized to elucidate the individual genes sets associated with CBX3 expression in the LIHC TCGA data, |NES| >1, FDR q value < 0.25 and P-value < 0.05 were considered as significance set-point for GSEA. Moreover, gene set variation analysis (GSVA) was performed to further identify significant differences in genome-regulated biological processes.
Statistical analysis
We analyzed the data by using the SPSS software (version 23.0, SPSS Inc., Chicago, IL) and GraphPad Prism 6.0 (GraphPad Software, Inc., LaJolla, CA, USA). The association of CBX3 expression with clinic-pathologic parameters in HCC was verified using the χ2 test. The continuous variables were calculated by Mann-Whitney U test and unpaired t test. Pearson’s correlation test was applied to analyze the correlation between CBX3 and Ki-67 mRNA expression, CBX3 and PCNA expression, CBX3 and miR139 mRNA expression. The log-rank tests and Kaplan-Meier methods were applied to evaluate the Patient survival. P < 0.05 was identified as statistical significance level for all analysis