Cell Culture and siRNA Transfection
The seminoma cell line TCAM-2 (seminoma) was donated by Professor Tang Yuxin.19 The human embryonic carcinoma cells line NCCIT (non-seminoma) was purchased from the American Type Culture Collection (ATCC, VA, USA). TCAM-2 cells and NCCIT cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM, GIBCO, USA) and RPMI-1640 medium (GIBCO, USA), respectively. All cells were cultured in a medium containing 10% fetal bovine serum (FBS, GIBCO, USA), 100 U/ml penicillin, and 100 µg/ml streptomycin (GIBCO) at 37°C and in a 5% CO2 incubator. Transfection was performed when the cells had grown to 60-80% confluence. The instructions provided with the lipofectamine 3000 transfection kit (cat no. L3000015, ThermoFisher) were strictly followed. The LINC00467 siRNA sequences were as follows: LINC00467-siRNA-1: GTCTTCAGGAAGCCAGACA, LINC00467-siRNA-2: GATGCTCTGTAAACCACAT. Both of The nucleotide sequence of the non-target negative control (NC) and LINC00467 siRNA sequences were synthesized by Ribobio (Guangzhou, China).
RNA extraction and qRT-PCR
The TRIzol method was used to extract RNA (cat no. 15596018, ThermoFisher). 1-2 μl of RNA was used to determine its concentration and quality using a spectrophotometer, and another 1-2 μl of RNA was used for gel electrophoresis to determine the quality of the RNA. A Roche reverse transcription kit (Transcriptor First Strand cDNA Synthesis Kit, cat no. 4897030001, Roche) was used for the reverse transcription PCR reaction. Levels of target mRNAs were measured using qRT-PCR (LightCycler 480 SYBR Green I Master, 10 x, cat no. roche04887352001, Roche) after transfection for 48 hours, and β-actin was used for normalization. The primers sequences see in Table 1.
MTT assay
The cells were seeded into 96-well plates at a concentration of 2000 cells per well in 3 replicate wells after transfection 48 hours. At 24, 48, 72, 96 and 120 hours, 20 μl of MTT solution (5 mg/ml) was added to each well. After incubation in a 5% CO2 atmosphere at 37°C for 4 h, the supernatant in each well was discarded. Then, 150 μl of DMSO was added to each well, and placed on a shaker for 1 min. The absorbance of each well was measured at 492 nm using a microplate reader. The absorbance value was used as the ordinate and the interval time was used as the abscissa, while the MTT cell growth curve was drawn using GraphPad Prism 5.0 software.
CCK8 assay
The cells were seeded into 96-well plates at a concentration of 2000 cells per well in 3 replicate wells after transfection 48 hours. At 24, 48, 72 and 96 hours, 10 μl of CCK-8 Solution (Sangon Biotech) was added to each well. After incubation in a 5% CO2 atmosphere at 37°C for 2 hours, the mixture was shaken for 1 min on a shaker in the dark. Then, absorbance at 450 nm was measured using a microplate reader. The absorbance value was used as the ordinate and the interval time was used as the abscissa. The CCK8 cell growth curve was drawn using GraphPad Prism 5.0 software.
Cell cycle assays
The cells were mixed with 95% ice-cold ethanol and fixed at 4°C for 16 hours after transfection 48 hours. Then, the cells were centrifuged at 300 g for 3 min and the supernatant was discarded. The cells were washed by resuspending them in ice-cold PBS. Then, 0.4 ml of propidium iodide staining solution (Cell Cycle and Apoptosis Analysis Kit, cat no. FXP021-200, Beijing 4A Biotech Co., Ltd) was added to each tube of cells slowly and the cell pellet was fully resuspended and incubated at 37°C for 30 minutes in the dark. The red fluorescence was detected at an excitation wavelength of 535 nm using a BD flow cytometry analyzer. The light scattering pattern was detected at the same time. Cell cycle analysis was performed using Modfit software.
Cell apoptosis assay
The cells were resuspended in a 1×Annexin-binding buffer and the cell concentration was adjusted to 1×106 cells/mL. Then, 100 µL of the cell suspension from each sample was taken and 5 µL of Alexa Fluor® 488annexin V and 1 µL of PI (100 µg/mL) (FITC Annexin V Apoptosis Detection Kit I, cat no. 556547, BD) was added. The mixture was kept to incubate at room temperature for 15 minutes in the dark. Then, 400 µL of 1×annexin-binding buffer was added to each sample and mixed by vortexing, and then a BD C6 flow cytometer was used for detection. Cell apoptosis analysis was performed using Flowjo 10 software.
DHT-treated cells
The cells were seeded into 6-well plates at an appropriate density. After the cells had reached 70% confluence overnight, the cells were washed twice with 1×PBS, and mediums containing 0 nM/mL, 1 nM/mL, and 5 nM/mL DHT (cat no. S4757, Selleck) were prepared using the complete medium as previously described. Then, 2 mL of complete medium was added at the above concentrations to each well on the six-well plate using three wells for each concentration. The cells were cultured in a 5% CO2 atmosphere at 37°C for 36 h and then the cells were collected.
Western blotting analysis
The protein precipitates were extracted using a RIPA protein lysate (cat no. 89900, ThermoFisher) containing a protease inhibitor phenylmethylsulfonyl fluorid (cat no. 36978, ThermoFisher, USA). Protein concentrations were determined using a BCA kit (ThermoFisher, USA). Then, the protein was subjected to SDS polyacrylamide electrophoresis and transferred onto a PVDF membrane (cat no. IPVH00010, Millipore). The PVDF membrane was blocked with 5% skimmed milk at room temperature. Then, the PVDF membranes were incubated overnight at 4°C with primary antibodies diluted with 5% skimmed milk. The primary antibodies used were mouse anti-PCNA Monoclonal antibody (1:2000, cat no. ab29, Abcam, USA) and rabbit anti-P21 Polyclonal antibody (1:1000, cat no. 10355-1-AP, Proteintech, Chian). Rabbit anti-Vinculin Monoclonal antibody (1:5000, cat no. ab129002, Abcam, USA) was used as the loading control. Then, the appropriate secondary antibody (CoWin Biosciences) was incubated with the PVDF membranes based on the genetic origin of the primary antibody. A gel imaging system was used to scan the protein bands using ECL reagents, and Vinculin was used as an internal reference.
RNA-sequencing
RNA sequencing was performed through de-ribosomal strand-specific library sequencing by first removing rRNA from total RNA to retain the mRNAs and ncRNAs. The enriched mRNAs and ncRNAs were fragmented into short fragments. The cDNA fragments were purified using a QiaQuick PCR extraction kit to repair the ends, add poly(A), and ligate the Illumina sequencing joints. The second-strand cDNA was digested with UNG (uracil-N-glucanase). Agarose gel electrophoresis was conducted to determine the size of the digested products. Then, the products were obtained and amplified using PCR and sequenced using an Illumina HiSeqTM 4000 platform (Gene Denovo, Guangzhou, China). The resulting cDNA library was sequenced using an Illumina Novaseq6000 system (Gene Denovo Biotechnology Co., Guangzhou, China).
Gene Set Enrichment Analyses
GSEA determines whether a pre-defined set of genes shows statistically significant differences in the gene expression profiling of the negative control group vs the LINC00467 silencing group. An annotated gene set (https://www.gsea-msigdb.org/gsea/msigdb/genesets.jsp?collection=CP:KEGG) was selected as the reference gene set. The Hiplot (https://hiplot.com.cn/) was used for the enrichment analysis at default parameters.
Statistical analysis
The Student’s t-test was used to determine the significance of differences between the two groups. GraphPad Prism Software 8.0 was used to analyze the statistics. A P value of <0.05 was considered to indicate a significant difference.