Gene expression profiles of cervical cancer
Gene expression profiles of cervical cancer were obtained from Gene Expression Omnibus (GEO) under the accession number GSE63514 [19]. In total, transcriptomes of 128 frozen cervical samples spanning normalcy, increasingly severe cervical intraepithelial neoplasia (CINI-CINIII), and cervical cancer were analyzed in this study. Gene expression profiles were measured by Affymetrix U133 Plus 2.0 microarray platform. The processed data were downloaded for further analysis.
Collection of histone acetylation-related genes
The histone acetylation-related genes were obtained from GO [20]. The genes in GO term ‘ACETYLTRANSFERASE_ACTIVITY’ were downloaded from MSigDB database [20]. In total, 88 genes were expressed in the transcriptomes of cervical cancers.
EMT scores
To calculate the EMT score for each sample, we first obtained the EMT-related genes from MSigDB [21]. Next, we performed the single sample gene set enrichment analysis (ssGSEA) to calculate EMT enrichment score for each patient [22].
Prioritization of genes in cervical cancer
To identify the histone acetylation-related genes that potentially correlated with EMT, we performed a two-step method to prioritize the genes. First, differential expression analysis was performed for patients with different states. Wilcoxon’s rank sum test was used to analyze the differences between the two states of patients in cervical cancer. Genes with p value ≤ 0.05 was considered as differentially expressed in cervical cancer. For all histone acetylation-related genes, we calculated the rank score R based on the combination of fold-change and p-value:
\({R}_{i}=-log10\) (\({\text{p}}_{i}\))\(*log2\left({FC}_{i}\right)\)
where \({\text{p}}_{i}\) is p-value for gene i and \({FC}_{i}\) is the fold-change comparison between cancer and normal samples.
Next, we identified the genes of which expressions were correlated with EMT scores in cervical cancer. Spearman correlation coefficients were calculated between the expressions of histone acetylation-related genes and EMT scores. Genes with p value ≤ 0.05 and absolute SCC ≥ 0.3 were identified. Finally, genes with top ranked R scores and correlated with EMT scores were overlapped.
Gene set enrichment analysis
For identifying the pathways potentially correlated with gene of interest, we first calculated the SCC between the expressions of candidate gene and all other genes. All protein coding genes were ranked based on the SCC and subjected into gene set enrichment analysis (GSEA) [22]. The EMT pathway was used as the pathway for analysis.
Tissue specimens
A total of 208 paraffin-embedded human cervical cancer tissues collected from January 2010 to December 2016 were obtained from the Southern Medical University Nanfang Hospital, Hainan Provincial People's Hospital and the First Affiliated Hospital of Hainan Medical University. Nineteen additional matched pairs of fresh cervical cancer tissue specimens (T) and adjacent noncancerous tissue (ANT) samples were obtained from the Department of Gynecological of Hainan Provincial People's Hospital from June to July 2019. All patients involved in this study were selected from the database and histologically confirmed as having cervical cancer, and none of the patients were treated with radiotherapy, immunotherapy or chemotherapy before surgery. For total protein isolation, 19 matched pairs of fresh cervical cancer tissue and ANT samples were obtained from patients immediately after surgery and snap-frozen at −80°C until use. The percentages of tumour purity in these tissues used for protein analyses were established by routine histopathological analyses [23]. The study was approved by the Research Ethics Committee of the Southern Medical University Nanfang Hospital, Hainan Provincial People's Hospital and First Affiliated Hospital of Hainan Medical University IRB (HYLL-2020-060). Informed consent was obtained from each participant.
Immunohistochemistry (IHC)
IHC was performed on paraffin-embedded human cervical tissue, ANT and tumour xenograft sections as previously described [23]. Primary antibodies, including anti-CSRP2BP (1:400; LS-B11653; LSBio), anti-N-cadherin (1:300; 13116S; Cell Signaling Technology), anti-E-cadherin (1:300; 3195; Cell Signaling Technology), and anti-Ki67 (1:400; sc-15402; Santa Cruz Biotechnology), were used to detect protein expression. For the negative controls, the procedures were performed without primary antibody. CSRP2BP staining was scored by two different pathologists who acted independently with regard to the evaluation of the intensity of staining and the proportion of positive staining. The staining index for CSRP2BP expression in cervical cancer was calculated by multiplying the two scores of the staining intensity and the proportion of positive cells. The median of all scores was used as a cut-off value for CSRP2BP. The optimal cut-off value was used as follows: a score of ≥ 6 was used to define tumours with high CSRP2BP expression, and a score of ≤ 4 indicated low CSRP2BP expression.
Cell culture
The human cervical cancer cell lines Hela (HPV18 +), SiHa (HPV -) and C-33A (HPV16 +) were obtained from the Chinese Academy of Sciences Cell Bank (Shanghai China), primary human cervical cancer cells (T1, T2, T3) were established based on previously reported methods [24]. All cell lines were subjected to high glucose Dulbecco’s modified Eagle’s medium (DMEM, Gibco, CA, USA) supplemented with 10% foetal bovine serum (FBS, Gibco, CA, USA) and antibiotics (50 U/ml penicillin and 50 μg/ml streptomycin; both from Gibco, CA, USA) and maintained in 5% CO2 and 37°C atmosphere.
Plasmids construction and transfection
The coding sequence of the human CSRP2BP gene (NM_001392073, Origene, USA) was amplified and subcloned into the Xhol and BamHI sites of the pLVX-AcGFP-N1 lentiviral vector (PT3994-5, Clontech, USA) to generate CSRP2BP expression plasmids. The Agel and EcoRI sites of the GV248-EGFP-puromycin lentiviral vector (GIDE77111, GENE, CN) were used to generate CSRP2BP shRNA constructs. The human CDH2 gene (NM_001308176, Origene, USA) was subcloned into the EcoRl and BamHl sites of the pSin-EF1α-puro lentiviral vector (SBI, USA). CSRP2BP mutants lacking the HAT domain (711-714 aa deleted) and N-cadherin-Luc reporter mutants lacking the SEB2 were generated using the KOD Plus Mutagenesis kit (Cade No. SMK-101, TOYOBO, Japan) according to the manufacturer’s instructions.
The vectors pMD2.G and psPAX2 were packaged in 293T cells using calcium phosphate transfection. Then, transduced cells were selected for 7 days with puromycin (P7255-25MG, Sigma, USA). The surviving cells were amplified by monoclonal culture. Hela and C-33A stable cell lines expressing CSRP2BP and shCSRP2BP were established (Hela/C-33A-CSRP2BP, Hela/C-33A-Vector, Hela/C-33A-shCSRP2BP and Hela/C-33A-shcon). Protein and mRNA of transfected cells were taken for real time-PCR and Western blotting analyses. The primers used in this study are listed in supplementary Table S1.
Western blotting
Western blotting was performed as described previously [25] by using anti-CSRP2BP (LifeSpan BioSciences, USA), anti-H4, anti-acetylated H4 on lysine 5 (H415Kac), anti-acetylated H4 on lysine 12 (H412Kac) (Abcam, USA), and anti-N-cadherin (Cell Signaling Technology, MA) antibodies. Next, the membranes were incubated with secondary antibody for 1 hour at RT, and then incubated with chemiluminescent substrate kit reagents (Millipore, USA); images were captured on a Tanon 4600SF instrument (Shanghai, China). The antibodies used in this study are listed in supplementary Table S2.
RNA isolation and quantitative real-time PCR
Total RNA was extracted using TRIzol reagent (Invitrogen Life Technologies, USA) based on standard procedures. Complementary DNA (cDNA) was prepared with the Prime Script® RT reagent kit (Takara, Japan) according to the manufacturer’s instructions. The primers used in this study are listed in supplementary Table S3. The expression level of gene mRNA was quantified using a SYBR® Premix E2x Taq TM II kit (Takara, Japan). The relative expression level was determined by normalizing the expression level of each target to GAPDH, and the relative mRNA fold change was determined using the 2 (-∆∆Ct) method. Samples were run in triplicate. Three independent experiments were performed.
Cell proliferation examination
For the cell growth curve, 1×104 cells were allowed to grow in 6-well plates and cultured for 6 days. The cells were counted every day to draw the cell growth curve. The 5-ethynyl-2’-deoxyuridine (EdU) assay was performed with the Cell-Light EdU Apollo 567 kit (RiboBio, China) according to the manufacturer’s instructions in vitro. All images were photographed with a fluorescence microscope (Olympus, DP72). For colony formation, cells were harvested and seeded into 6-well plates with a mount of 1 × 103 cells/well. On day 10, the cell colonies were stained with Giemsa stain for 15 min after fixation with 4% paraformaldehyde (Biosharp, China) for 30 min. Colonies with > 50 cells were counted. Three independent experiments were performed.
Wound healing assay
Wound healing assays were established by using Ibidi Culture Insert chambers (Ibidi, Germany) following the manufacturer’s protocol. A total of 45 × 104 cells were added to each well of the chamber. After 24 h, wound closure was monitored, and images were captured at different time points using an Olympus microscope (Olympus). Data were analyzed by using previously published methods .
Transwell migration assays
Cell invasion assays were performed using 12-well tissue culture plate inserts (8.0 μm pores, BIOFIL, China) precoated with Matrigel (BD Biosciences). First, cells suspended in 200 μL of serum-free medium were plated in the upper chambers, whereas 600 μL of medium supplemented with 10% FBS was placed in the lower chambers. After 24 h of incubation, the cells on the lower surface of the membrane filter were fixed and stained and then counted with an inverted microscope (Olympus, IX71).
Immunofluorescence
Cells grown on cover slides were fixed with methanol and acetone (1:1) for 20 min at -20°C, permeabilized with 0.5% Triton X-100 for 20 min, blocked with 5% BSA (Beyotime, China) in phosphate buffered saline (PBS) containing 0.1% Tween-20 for 1 h, and then incubated with a primary antibody overnight at 4°C. Subsequently, the slides were incubated with Alexa Flour® 488 IgG anti-mouse (Abcam, US) or Alexa Flour® 594 IgG anti-rabbit (Abcam, US) at room temperature for 1 hour. DAPI was used to stain the nuclei for 5 min. Fluorescence images were taken using confocal microscopy (Olympus Fluoview FV3000).
Flow cytometry and chemoresistance model in vitro
Flow cytometry was performed using a BD FACS Aria II cell sorter (Becton Dickinson, San Jose, CA) to analyse the cell cycle through propidium iodide (Sigma, China) staining. Modfit LT 3.1 trial cell cycle analysis software was used to analyse the cell cycle. The cells were plated in 6-well plates (1 × 105 cells/well) and cultured until they reached 90% confluency. Through flow cytometry, the annexin V+/PI cells were analysed after the indicated cells were treated with cisplatin (20μg/ml, 40μg/ml, 80 μg/ml) for a 24 h culture.
Coimmunoprecipitation (Co-IP) assay
Plasmid vectors expressing Flag-HA-tagged SMAD3 and Flag-HA-tagged SMAD4 were cotransfected into Hela cells with HA-tagged CSRP2BP by using Lipo2000TM Transfection Reagent (Invitrogen, CA, USA) according to the manufacturer’s instructions. Hela cells were lysed and incubated with RAPI (Biosharp, China) lysis fluid containing 1× PMSF (Cell Signaling Technology, MA, USA) and 1× protease inhibitor cocktail (Cell Signaling Technology, MA, USA). After centrifugation, the protein supernatant was collected and incubated with the corresponding antibody at 4°C for 2 hours. The antigen-antibody complex was precipitated with protein A/G (Invitrogen, CA, USA), and Western blotting was performed to examine the target proteins.
siRNA transfection
siRNA duplexes against N-cadherin and SMAD4 were transfected into Hela-CSRP2BP, Hela-Vector cells by using LipofectamineTM RNA iMAX Transfection Reagent (Invitrogen, CA, USA) according to the manufacturer’s instructions. The siRNA duplex sense sequences were as follows: si-N-cadherin: 5’-CCAGUGACUCUUAAGAGAA-3’, si-SMAD4: 5’-CCACCAAGUAAUCGUGCAU-3’.
Luciferase reporter assays
Regions of the CDH2 promoter (~2 kb) were amplified using the primers and subcloned into the PLG3-basic luciferase reporter plasmid to synthesize the pGL-3-N-cadherin promoter plasmid. The coding sequences of the human CSRP2BP gene (NM_001392073, Origene, USA) and SMAD4 gene (NM_000018.10, Origene, USA) were amplified and subcloned into the Xhol and BamHI sites of the PCGN vector (PT3994-5, Clontech, USA). Luciferase activity was measured as described previously [28].
Xenograft models
BALB/c-nu mice (n=20, 5-6 weeks of age, Gem Pharmatech. Co. LTD) were kept in aseptic conditions under constant temperature and humidity. The mice were randomly divided into four groups, and each mouse received a groin subcutaneous injection of a 100 μL suspension of 1×106 cells. Tumour growth was detected with callipers every 2 days, and tumour volume was calculated using the following formula: Volume = (length×width2)/2. Magnetic resonance imaging (MRI) was used to evaluate the tumours in the mice. To further evaluate the metastatic potential of CSRP2BP, mice (n=5) were transplanted with 1x106 cells suspended in 100 μL PBS by tail intravenous injection. Six weeks after transplantation, all mice were sacrificed, and the tumours were harvested and imaged by a chemiluminescent imaging system (Sacecreation).
Chromatin immunoprecipitation (ChIP)
Cells were fixed with 37% formaldehyde for 10 min, treated with 0.125 M glycine for 5 min and centrifuged at 3000 × g at 4 °C for 5 min to collect a crude nuclear fraction. The nuclear pellet was incubated with 1% SDS lysis buffer and sonicated to shear genomic DNA into 100~400 bp fragments. Genomic DNA fragments were transferred to slide-A-LyzerTM G2 (Invitrogen Life Technologies, CA, USA) at 4 °C for 4 h. Immune complexes were precipitated with protein A/G beads (Invitrogen Life Technologies, USA), and soluble chromatin complexes were immunoprecipitated with human IgG antibody (Proteintech), H4ac antibody (Active Motif) or CSRP2BP antibody (Life Span Biotechnology) in ChIP dilution buffer overnight at 4 °C. The beads were sequentially washed with a low salt buffer, a high salt buffer, LiCl wash buffer, and TE buffer. The immunoprecipitated chromatin complexes were eluted in ChIP direct elution buffer at 65 °C for 30 min and incubated overnight at 65 °C to cross-link the chromatin complexes. DNAs were isolated using a QIAGEN DNA kit (28106, Germany). The extracted DNA was analysed by real-time PCR. Primers to detect N-cadherin promoter occupancy were listed in supplementary Table S4.
RNA-seq
Total RNA from cells for RNA sequencing was isolated using TRIzol reagent (Invitrogen Life Technologies, USA) based on standard procedures. Subsequently, an Agilent 2100 bioanalyzer and a NanoDrop 2000 were used to examine quality. Libraries were constructed using the standard Illumina library construction process. Each library was sequenced on an Illumina NovaSeq 6000 in 150 PE mode by Beijing Berry Genomics Co., Ltd. (Beijing, China).
Statistical analyses
All statistical analyses were performed using the SPSS software package (version 19.0, SPSS, Inc.) and Prism 5.0 software (GraphPad, La Jolla, CA, USA). The data are presented as the mean ± SD of at least three independent experiments. The independent sample t test was used for comparing groups to identify significant differences. The Kaplan‒Meier method was used for PFS and OS analysis, and significance was determined by the log-rank test. Multivariate logistic regression was performed to identify the independent risk factors related to the prognosis of cervical cancer. The relationships between CSRP2BP expression level and clinicopathological features were tested by the χ2 test or Fisher’s exact test. The results were considered statistically significant at P < 0.05.