MicroRNA-153 functions as a tumor suppressor by targeting SET7 and ZEB2 in ovarian cancer cells
- Authors:
- Published online on: May 5, 2015 https://doi.org/10.3892/or.2015.3952
- Pages: 111-120
Abstract
Introduction
MicroRNAs are a cluster of conserved, small, non-coding single-stranded RNAs (18–25 nucleotides), the function of which are to modulate gene expression by binding to the target gene with complementary recognition sequences of 3′ untranslated regions (3′-UTRs), leading to target mRNA degradation or negatively regulating translational efficiency (1–3). Growing amounts of evidence indicate that miRNA expression is altered in almost all types of cancer (4–7). The deregulation of miRNAs plays an important role in various cellular processes, such as proliferation, the cell cycle, apoptosis and metastasis contributing to tumorigenesis (8,9).
Despite growing knowledge in understanding ovarian cancer etiology, of which more than 85% are of epithelial origin. Epithelial ovarian cancer (EOC) remains the most lethal form of gynecological malignancy in the USA (10–12). EOC are classified into distinct histologic types including serous (60% of all cancers), mucinous, endometrioid and clear cell (less common histologies) (13,14). Shih and Kurman divided EOC into 2 types (15), type I includes low-grade serous, low-grade endometrioid, mucinous and clear cell carcinomas, and type II EOC includes the high-grade types (15).
The molecular mechanisms that contribute to the tumor progression such as proliferation and metastasis still need further exploring. We focused on ZEB2/SIP1, which are potent repressors of E-cadherin expression, through binding to CACCT(G) motif in the E-cadherin promoter (16) and considered to be a key factors of epithelial-mesenchymal transition (EMT) (17). EMT are believed to be the initial step of tumor metastasis, during EMT epithelial cells lose their differentiated epithelial characteristics, and acquire mesenchymal features, such as motility, and invasiveness (18). ZEB2 plays important role in the development of a variety of cancers, such as gastric, squamous, breast, non-small cell lung and ovarian carcinomas (19–21). Besides E-cadherin, other genes coding for crucial proteins such as plakophilin 2 involved in tight junctions were found to be repressed by ZEB2 (17). Recently, vimentin was reported to be upregulated by ZEB2, another mesenchymal marker, which is associated with breast tumor cell migration and invasion in a study by Bindels et al (22).
SET domain containing 7 (SET7) is a lysine methyltransferase with the function of methylation histone and non-histone proteins. By which it has diverse functions in transcription regulation, diabetes, DNA repair, tumor metastasis, proliferation and genome integrity (23–26). The activity of SET7 is tightly controlled through post-translational modifications, including ubiquitination, phosphorylation and sumoylation (27,28). Yet, the role of microRNAs in the regulation of SET7 has not been discovered.
Considering EMT is a process regulated by numerous factors, it is reasonable to hypothesize that different miRNAs are involved in the regulation. However, although the miR-200 familys in EMT have been well discussed, the roles of other miRNAs are still poorly understood (29,30). Thus, there is an urgent need to better understand the role of miRNA in EOC to develop novel therapeutics for this disease.
Materials and methods
Cell culture
Human ovarian serous cystic adenocarcinoma cell line OVCAR3 and human serous papillary cystic adenocarcinoma cell line SKOV3 were purchased from the American Tissue Type Collection (Manassas, VA, USA). Both cell lines are suitable transfection hosts. Normal epithelial ovarian cells (NOE095 and HOSEpiC) were obtained from the Chinese Academy of Sciences. All cells were cultured in RPMI-1640 medium supplemented with 10% fetal calf serum (Gibco), 100 IU/ml penicillin and 100 IU/ml streptomycin. These cell lines were grown at 37°C in a humidified atmosphere with 5% CO2. For the transfections, cells were grown to 70% and transfected with plasmids using Lipofectamine 2000 (Invitrogen, USA) according to the manufacturer’s recommendation.
Clinical specimens
A total of 60 cases of ovarian cancer specimens and their adjacent normal tissues were obtained from Xiangya hospital. The age ranged from 28 to 55, the average was (34±8). The patients who had received radiation or chemotherapy prior to the surgery were excluded. The tissue samples were stored in liquid nitrogen. The survival times were calculated from the operation day to death, via the evaluation of recurrence and metastasis. Samples were selected from patients with complete clinicopathologic information. The study was approved by the Xiangya hospital ethics committee.
Antibodies and siRNAs
Primary antibodies used were rabbit anti-ZEB2 (Sigma-Aldrich), mouse anti-SET7 (Abcam) and rabbit anti β-actin (Sigma-Aldrich). β-actin was used for normalization. The small interfering RNAs (siRNA) targeting human ZEB2, SET7, control siRNA were from (Sigma-Aldrich), miR-153 mimics were synthesized by Shanghai GeneChem Inc. (Shanghai, China), miR-153 inhibitors and inhibitor negative control (anti-miR-NC) were obtained from Dharmacon.
Transfection of miRNA mimics and inhibitors
Cells were seeded in a 6-well plates and transfected with synthetic miRNA-153 mimics or miR-153 inhibitors or miR-control or inhibitor-control at 3×105 cells/well with a final concentration of 100 nM using Lipofectamine 2000, according to the instructions provided by the manufacturer. Total RNA were collected 2 days post-transfection, and protein 3 days, transfection efficiency was monitored by qRT-PCR. The sequences of miR-153 were as follows: sense, 5′-UUGCAUAGUCACAAAAGUGAUC-3′ and antisense, 5′-GAUCACUUUUGUGACUAUGC AA-3′. For miRNA analysis, real-time PCR was performed using PrimeScript® miRNA RT-PCR kit (Takara) according to the manufacturer’s instructions. All miRNA data are expressed relative to a U6 small nuclear RNA from the same sample.
RNA extraction and real-time PCR
Total RNA was extracted using TRIzol (Invitrogen), and total RNA was extracted using a high Pure miRNA Isolation kit (Roche) according to the manufacturer’s instructions, for analysis of SET7 and ZEB2 messenger RNA (mRNA) expression, RNA were reverse transcribed to cDNA using 1 µg of total RNA with M-MLV reverse transcriptase, according to the manufacturer’s instructions. The specific primers for SET7, ZEB2 and β-actin were as follows: SET7 forward, 5′-CCTCACTTTGAACTGATGCC-3′ and reverse, 5′-CAGCAACATAAACCCTTTCTG-3′; ZEB2 forward, 5′-AGGAGCTGTCTCGCCTTG-3′ and reverse, 5′-GGCAAAAGCATCTGGAGTTC-3′; and β-actin forward, 5′-TGGCACCCAGCACAATGAA-3′ and reverse, 5′-CTAAGTCATAGTCCGCCTAGAAGCA-3′; β-actin served as the internal control.
Plasmid construction and luciferase assays
The wild-type and mutant SET7 or ZEB2 3′-UTR were amplified by PCR and cloned in pMIR-Report (Ambion) to generate a series of reporter constructs with firefly luciferase. The luciferase assays were performed in OVCAR3 cells as described previously, OVCAR3 cells treated with control, miR-153 mimics, or miR-153 inhibitors were transfected with wild-type or mutants of SET7 or ZEB2 3′-UTR luciferase reporters along with Renilla plasmid, using Lipofectamine LTX-Plus (Invitrogen). Forty-eight hours after transfection, the firefly and Renilla luciferases were assayed according to the manufacturer’s protocol (Promega), and the firefly luciferase activity was normalized to that of Renilla luciferase. Each experiment was repeated in triplicate. The amount of DNA was kept constant by addition of empty vector in each transfection.
Western blotting
Cells were harvested 48 h after infection in each group and protein concentration was determined using the bicinchoninic acid (BCA). Subsequently, 30 µg protein were run by 10% SDS-PAGE gel and transferred to NC membranes. NC membranes were blocked by 5% skim milk for 1 h, then incubated overnight at 4°C with primary antibodies, including ZEB2 (1:1,000), SET7 (1:1,000) and β-actin (1:500). Goat anti-rabbit secondary antibodies (1:5,000) or goat anti-mouse secondary antibodies (1:3,000) and Western Blotting Luminol Reagent (Santa Cruz Biotechnology) was used to visualize the protein bands.
Colony formation assay
A total of 5,000 cells were inoculated in 6-well plates in 1.5 ml of RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS), after the infection for 3 days. The medium was changed at the interval of 3 days; after 10 days of culturing, the colonies (which were a cluster of cells seen under the microscope) formed, the plates were washed with phosphate buffered-saline (PBS) and fixed in 4% paraformaldehyde at 37°C for 30 min, after which the colonies were stained with 0.005% crystal violet (Sigma) in PBS for 15 min, washed and then air-dried. The colonies were counted using microscopy (Olympus, Tokyo, Japan). This experiment was performed in triplicate.
Wound-healing assay
SKOV3 cells were seeded in 12-well plates and cultured to form a confluent monolayer. Wounds (2-mm) were made with a sterile plastic scraper, the floating cells were washed away three times with PBS. Images were captured at indicated time points after wounds were made. After incubation in a serum-free medium for 24 h, to exclude the impact of serum medium on proliferation, cultures were observed and images were captured under a microscope. At least five randomly chosen areas were measured, and repeated three times.
Transwell invasion assay
The Transwell invasion assays were performed using the Transwell chamber (8-µm pore size, for 24-well plates; Millipore) with a Matrigel-coated filter. OVCAR3 cells were transfected with control, miR-153 mimics or miR-153 inhibitors with/without ZEB2 cDNA lacking 3′-UTR. A total of 100 µl of the cell suspension (50,000 cells) with serum-free medium was added to the upper chamber of the Transwell, and 500 µl of RPMI-1640 containing 10% FBS was added to the lower compartment. After incubation for 24 h, cells on the upside were removed using cotton swabs, and the invasive cells on the lower side were fixed, stained with 0.1% crystal violet solution, and counted using light microscopy. The experiments were repeated three times.
Bioinformatics analysis and statistical analysis
The bioinformatics method was used to predict the potential target genes of miR-153. The microRNA.org (http://www.microrna.org/microrna/), miRDB (http://mirdb.org/cgi-bin/) and TargetScan (http://www.targetscan.org/) databases were used, SET7 and ZEB2 was considered as the candidate gene.
Statistical significance was assessed by comparing mean values (± SD) using a Student’s t-test for independent groups. P<0.05 were considered to indicate a statistically significant result. One-way analysis of variance (ANOVA) with SNK-q test for multiple comparisons was used to analyze the data from the Transwell migration assay and western blotting using SPSS 15.0 software. *P<0.05, **P<0.01.
Results
miR-153 is a potential tumor suppressor in ovarian cancer
In order to explore the role of miR-153 during the progress of ovarian cancer, we first enrolled 60 ovarian cancer patients. They were divided into two groups based on their miR-153 expression levels: those with less than median of miR-153 expression levels and those with more than or equal to median of miR-153 expression levels. The higher expression of miR-153 indicates a better overall 5-year survival (the hazard ratio, 2.4183, P<0.05) Kaplan-Meier curves were drawn, the details are shown in Fig. 1A.
To investigate the role of miR-153 in human ovarian cancer, the expression of miR-153 was compared using qRT-PCR in ovarian cancer samples and corresponding noncancerous tissues. The results showed that expression level of miR-153 in ovarian cancer was significantly lower (median, −1.5099; max, −0.97469; min; −2.0385) than in non-cancerous tissues (median, 1.1019]; max, 3.3357; min, −1.2377) (P<0.01, Fig. 1B). Growth assays in cells transfected with miR-control or miR-153, OVCAR3 cells with miR-153 showed an obvious growth inhibition (Fig. 1C). To further explore the miR-153 impact on migration and invasion, a wound-healing assay was conducted. As shown in Fig. 1D, 24 h after the wound were created and measured, cells with miR-153 were significantly impaired in wound recovery, compared with the control cells. To further assess the effects on cell invasion, Transwell assay was performed. Migrated cells infected with miR-153 counts for one third of those infected with miR-control (Fig. 1E), the above data show miR-153 functions as a potential tumor suppressor in ovarian cancer.
miR-153 regulates the expression and mRNA degradation of the target gene SET7
As reported, miRNAs silence genes either by translational inhibition or mRNA destabilization (31,32). Connecting with the bioinformatic prediction, with analyses based on three public algorithms (TargetScan, PicTar and miRanda), indicated that the SET7 3′-UTR harbors two potential miR-153 target sites (positions 46–52 and 4732–4738), both positions are highly conserved regions in different species (Fig. 2A and B). These sites are completely complementary to the human miR-153 heptamer motif 5′-UGCAUAG-3′.
To prove the proposition that SET7 is a downstream target of miR-153, reporter assays were carried in OVCAR3 cells. Luciferase gene is driven by wild-type or mutated SET7 3′-UTR sequences, including the full-length or three deletions of the wild-type SET7 3′-UTR or 2 mutants (with three point mutations) of SET7 3′-UTR (Fig. 2C, left panel). The results demonstrated >60% reduction in luciferase activity with the full-length wild-type (wt-1) SET7 3′-UTR in OVCAR3 cells transfected with miR-153. Consistent with our prediction, the site A including the position 46–52 or site C including the position 4732–4738 plays a more important role in the binding of miR-153 to SET7 3′-UTR, as there was more evident decrease in luciferase activity with wt-2, wt-4 compared with that of wt-3 (Fig. 2C, right panel), point mutation of mut-1 with site A and mut-2 with site C disrupted miR-153 repressive activity, further indicated the binding of miR-153 to sites A and C of SET7 3′-UTR was specific. Taken together, these results suggest that miR-153 binds to SET7 3′-UTR. We then investigated whether binding to the SET7 3′-UTR has an effect on the expression of SET7 mRNA and protein. For this purpose, OVCAR3 and SKOV3 cells were transfected with control or miR-153, the results showed that miR-153 overexpression was decreased by more than half in SET7 mRNA in the two cell lines, respectively (Fig. 2D, left panel), and western blot analysis showed an obvious reduction of SET7 protein expression (Fig. 2D, right panel). Consistently, OVCAR3 and SKOV3 cells transfected with miR-153 inhibitors resulting in an increase in SET7 mRNA by real-time quantitative PCR (qPCR) (Fig. 2E, left panel) and a significant rise in SET7 protein expression by western blotting (Fig. 2E, right panel). To further evaluate the impact of miR-153 on SET7 mRNA stability, OVCAR3 and SKOV3 cells treated with transcription inhibitor actinomycin D were then transfected with miR-153 mimics or miR-153 inhibitors. Real-time qPCR showed that miR-153 overexpression led to a reduced SET7 mRNA half-time (from 8 to4 h) while an increased SET7 mRNA half-time was due to miR-153 depletion (Fig. 2F), further supporting the fact that miR-153 represses SET7 expression through destabilization of SET7 mRNA.
ZEB2 is a downstream target of miR-153 directly binding to its 3′-UTR
To identify ZEB2 as a target of miR-153, using bioinformatics method as the way to discuss SET7, also two highly conserved regions were found located in the ZEB2 3′-UTR (positions 689–695 and 191–197), (Fig. 3A and B). The motif 5′-UGCAUA-3′ of human miR-153 are fully complementary with ZEB2 3′-UTR.
Further, reporter assays were carried out in OVCAR3 cells with the luciferase gene driven by either four wild-type or two mutated ZEB2 3′-UTR sequences (Fig. 3C, left panel), the results indicated the sites A (including position 191–197) and B (including position 689–695) play a more important role in the binding of miR-153, as there were more evident decreases in luciferase activity with wt-2, and wt-3 compared with that of wt-4. Further, the relative mutation (mut-1 with site A and mut-2 with site B) blocked miR-153 repressive activity on reporter gene expression (Fig. 3C, right panel). Real-time quantitative PCR and western blot analysis showed OVCAR3 and SKOV3 cells with miR-153 overexpression (Fig. 3D) or miR-153 inhibition (Fig. 3E), the mRNA or protein level of ZEB2 reduced or increased. The influence of ZEB2 mRNA stability by miR-153 were further measured, as well as SET7, miR-153 overexpression also led to a reduced ZEB2 mRNA half-life (from 12 to 6 h) while miR-153 inhibition was associated with an increased ZEB2 mRNA half-life (Fig. 3F). As a conclusion, the miR-153 represses ZEB2 expression may also be through destabilization of ZEB2 mRNA, similarly to SET7.
miR-153 suppresses proliferation and invasive potential of ovarian cancer cells by downregulating SET7 and ZEB2
Furthermore, to examine whether miR-153 regulated EOC cell line proliferation by suppressing SET7 in vitro, proliferation assay was detected by colony formation assay. OVCAR3 cell lines were transfected with NC (mimics negative control), miR-153 mimics, miR-153 mimics plus SET7 overexpression, miR-153 mimics plus ZEB2 overexpression, or inhibitor NC, miR-153 inhibitor, miR-153 inhibitor plus siSET7, miR-153 inhibitor plus siZEB2, respectively. The transfection efficiency was validated using qRT-PCR (Fig. 4A). The colony formation assay showed that miR-153 overexpression or downregulation affected cell proliferation, the upregulation of miR-153 inhibition the colony formation was reduced by SET7 overexpression and the downregulation of miR-153 expression promoted proliferation ability could be blocked by the additional SET7 knockdown (Fig. 4B). The above data suggested that miR-153 that could inhibit OVCAR3 cell line proliferation by the suppression of SET7 in vitro.
We investigated the effect of miR-153 overexpression on cell lines invasion using wound healing or Transwell invasion assay (Fig. 1D and E). Considering ZEB2 as a key regulator in EMT (20), and as a potential target of miR-153, in the present study, we further proved the effect of gain-of-function or loss-of-function of miR-153 and ZEB2 as downstream target genes on the invasive potential in SKOV3 cells by wound-healing assays.
The results showed that miR-153 inhibitor-treated cells were more efficient in wound healing, whereas cells treated with miR-153 inhibitor plus ZEB2, loss of function was resistant to wound healing to certain degree, compared with miR-153 inhibitor only, the representative images (left panel) and the overall tendency was compared between NC (mimics negative control), miR-153 mimics, miR-153 mimics plus ZEB2 overexpression, or inhibitor NC, miR-153 inhibitor, miR-153 inhibitor plus siZEB2, respectively (Fig. 4C). In addition, Transwell invasion assays showed that miR-153 knockdown promoted the invasion by 4-fold. Moreover, miR-153-suppressed EMT of EOC cancer cells was probably mediated by ZEB2, as downregulation of ZEB2 was able to rescue the effect of knockdown miR-153 on tumor migration and invasion, however, the overexpression of miR-153 was blocked by ZEB2 upregulation (Fig. 4D). Together, these results support the argument that miR-153 suppresses EMT and invasion of ovarian cancer cells and is at least partially, mediated by targeting ZEB2.
SET7 and ZEB2 are negatively correlated with miR-153 expression in human ovarian cancer and indicate a worse survival
Moreover, an inverse correlation was observed between miR-153 and SET7 (R=0.7141; P<0.001; Fig. 5A, left panel), or miR-153 and ZEB2 (R=0.7669; P<0.0001; Fig. 5A, right panel) in ovarian cancer samples. To further explore the role of miR-153 and SET7 or ZEB2 expression in ovarian cancer tumorigenesis, the expression of miR-153 and SET7 or ZEB2 was examined in two ovarian cancer cell lines (OVCAR3 and SKOV3) and two normal ovarian cell lines using qRT-PCR. As shown in Fig. 5B, left panel, the expression of miR-153 was substantially reduced in OVCAR3 and SKOV3 cell lines derived from ovarian cancer, compared with the normal NOE095 and HOSEpiC cell lines. However, the expression of SET7 and ZEB2 was significantly increased in OVCAR3 and SKOV3, comparing with NOE095 and HOSEpiC. The tendency was negatively correlated with miR-153 (Fig. 5B, middle and right panel). The result of correlation analysis suggested a potential functional link of miR-153 and SET7, or miR-153 and ZEB2. Further, the patients collected were divided into different groups, based on the single SET7 or ZEB2 expression level, Kaplan-Meier curves were drawn (Fig. 5C). As the data showed, the higher expression of SET7 indicates a worse 5-year survival (the hazard ratio, 2.3353, P<0.05) (Fig. 5C, upper panel). Similarly, patients with more than, or equal to median, of ZEB2 expression also had a worse 5-year survival (the hazard ratio, 2.4134, P<0.05) (Fig. 5C, lower panel). These results indicated that by downregulation of SET7 and ZEB2, miR-153 may be involved in the proliferation and metastasis of ovarian cancer.
Discussion
microRNAs have been reported to be upregulated or downregulated in a various disease states and specific cell types, the action of microRNA as either oncogenes or tumor suppressors depended on the target gene (33,34). By regulating the target genes with binding to their 3′-UTR, miRNAs have been proved to play important roles in different cancers (6,35,36). Accumulating evidence reveals the crucial role of miRNAs involved proliferation, invasion, prognosis and other biology processes (2). The concept of ZEB2 as powerful regulator of EMT has been widely accepted, and several miRNAs have also been described as crucial EMT regulators (19).
In the present study, the expression of miR-153 was lower in EOC tissues than that in the corresponding adjacent areas, and the upregulation of miR-153 inhibited the proliferation and invasion of OVCAR3 cell lines (Fig. 1C–E), while the effect of miR-153 overexpression was the reverse (Fig. 4B–D). Furthermore, we also discovered that the overexpression of miR-153 diminished but the knockdown of miR-153 increased SET7/ZEB2 expression level in OVCAR3 and SKOV3 cell lines. By directly binding the 3′-UTR of SET7/ZEB2, miR-153 promoted SET7/ZEB2 mRNA degradation. Ectopic miR-153 expression regulated the expression level of SET7 in the cell lines (OVCAR3 and SKOV3). SET7 and ZEB2 as potential targets of miR-153 in ovarian cancer was proved as miR-153 inhibited ovarian cancer proliferation and invasion via repression of SET7 and ZEB2 in vitro. Furthermore, we discovered that silencing of SET7 or ZEB2 partially abolished the enhancement of cell proliferation and invasion induced by downregulated miR-153, confirmed SET7 and ZEB2 as downstream target genes of miR-153. In the present study, we found that SET7 and ZEB2 were negatively associated with miR-153 in EOC tumor tissue and cell lines, higher expression of SET7 or CARM1 indicated a worse overall 5-year survival. On the contrary, the higher expression of miR-153 indicates a better overall 5-year survival. The above finding indicated that miR-153 contributes to regulating epithelial-to-mesenchymal transition (EMT). Since we are unsure whether miR-153 has other targets related to EOC proliferation and invasion, the changes in the development of EOC should not be attributed as the alteration of a small number of genes. Thus, further exploration is necessary of the potential role of miR-153 contribution to EOC. In future, miR-153-SET7 and miR-153-ZEB2 pathways may be exploited in a therapeutic approach for the treatment of ovarian cancer.
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