E2F8, a direct target of miR-144, promotes papillary thyroid cancer progression via regulating cell cycle
- Jing Sun†1,
- Run Shi†2,
- Sha Zhao3,
- Xiaona Li4,
- Shan Lu5,
- Hemei Bu1,
- Xianghua Ma1Email author and
- Chuan Su6Email author
© The Author(s). 2017
Received: 10 December 2016
Accepted: 16 February 2017
Published: 7 March 2017
Thyroid cancer is the most common malignancy of endocrine system, and papillary thyroid cancer (PTC) is the most common subtype. E2F8, a novel identified E2F family member, was reported to associate with progression of several human cancers, however, its clinical significance and biological role in PTC remain unknown.
E2F8 or miR-144 expression profiles in PTC tissues were obtained from The Cancer Genome Atlas (TCGA) datasets, and the correlation of E2F8 expression with clinicopathological features was analyzed in a cohort PTC patients. The effects of E2F8 and miR-144 on proliferation were evaluated both in vitro and in vivo. Luciferase reporter assay was used to determine E2F8 was a direct target of miR-144.
E2F8 was widely upregulated in PTC tissues, and overexpression of E2F8 was correlated with more aggressive clinicopathological features. In contrast, we found that silence of E2F8 significantly suppressed proliferation of PTC cells by inducing G1-phase arrest via downregulating Cyclin D1 (CCND1) both in vitro and in vivo. We also identified miR-144 as a tumor-suppressive microRNA that directly targeted E2F8 to inhibit proliferation of PTC cells in vitro and in vivo. Moreover, miR-144 was widely downregulated in PTC, where its expression correlated inversely with E2F8 expression.
Our results demonstrate a new miR-144/E2F8/CCND1 regulatory axis controlling PTC development, which may offer a potential prognostic and therapeutic strategy.
KeywordsE2F8 miR-144 Papillary thyroid cancer (PTC) TCGA Proliferation Cell cycle
Thyroid cancer is the most common malignancy of endocrine system, and its incidence has increased rapidly worldwide in the past few decades . Thyroid cancer is classified into four types: papillary, follicular, medullary and anaplastic thyroid cancer. Papillary thyroid cancer (PTC) is the most common subtype, accounting for more than 80% of all thyroid cancers, and associates with a favorable therapeutic response and prognosis . However, in the case of aggressive PTC and certain PTC variants, a regional recurrence or distant metastasis is observed in 5–20% of the patients who have undergone total thyroidectomy [3, 4]. Therefore, novel biomarkers and potential therapeutic targets are eagerly needed to provide better follow-up treatment.
As known, E2F family function as transcription factors that bind to target promoters and regulate their expressions . To date, eight members, E2F1-8, have been recognized. In general, E2F1-3 are considered as transcriptional activators, whereas E2F4-7 play an inhibitory role in transcriptional expression of downstream target genes [6–8]. However, the function of a novel member, E2F8, is still poorly understood. It has been reported that E2F8, in combination with E2F7, is required for embryonic development in mice [9, 10], angiogenesis  and lymphangiogenesis  in zebrafish. Moreover, E2F8 expression has been found to be upregulated in ovarian cancer , hepatocellular cancer , lung cancer  and breast cancer . Furthermore, E2F8 also promoted cancer malignant progression in breast cancer , prostate cancer  and hepatocellular cancer , and served as a therapeutic target in lung cancer . These findings have indicated that E2F8 might play a role in the development of cancer. However, the clinical significance and biological function of E2F8 in PTC has not yet been investigated.
MicroRNAs (miRNA) are small noncoding RNAs that can modulate the expression of cognate target genes by binding to their mRNA 3’-untranslated region (3’-UTR), resulting in either translational inhibition or mRNA cleavage . Accumulating evidence indicates that miRNAs can act in human carcinogenesis as novel types of tumor suppressors or oncogenes [19–21]. Several studies have shown that miRNAs have an important role in PTC progression [22–24]. Hence, we are interested in whether E2F8 expression is regulated by certain miRNAs as a posttranscriptional regulation mechanism in PTC.
In this study, we provide the first evidence that E2F8 overexpression is associated with more aggressive clinicopathological features in PTC. We show that silence of E2F8 inhibited proliferation of PTC cells both in vitro and in vivo. Moreover, we demonstrate that E2F8 can promote G1/S transition via upregulating Cyclin D1 (CCND1) at least. We further demonstrate that E2F8 is a direct functional target of miR-144, which controls PTC cell proliferation both in vitro and in vivo. Our results suggest that the miR-144/E2F8/CCND1 axis might function as a key pathway regulating tumor cell proliferation during PTC development.
Data sources and bioinformatics
Two TCGA datasets named TCGA_THCA_miRNA_HiSeq-2015-02-24 and TCGA_THCA_exp_HiSeqV2-2015-02-24 were downloaded at the website of the UCSC cancer browser (https://genome-cancer.ucsc.edu/) , containing 59 paired PTC tissues and adjacent normal tissues. All normalized gene expression values can be obtained from “genomicMatrix” files.
A list of 143 genes with highest co-expression correlation (Pearson r value > 0.5) (Additional file 1: Table S1) with E2F8 were submitted to DAVID Bioinformatics Resources 6.7 (http://david.abcc.ncifcrf.gov/)  for Gene Ontology (GO) enrichment analysis.
In this study, we collected 64 paired cases of PTC and adjacent normal tissue samples from patients who underwent surgical resection at The First Affiliated Hospital of Nanjing Medical University (Nanjing, China) from 2012 to 2015. Informed written consent for scientific use of biological material was obtained from each patient, and this study was approved by the Ethics Committee of Cancer Institute of Jiangsu Province. All patients’ clinicopathological parameters, including age, gender, primary tumor size, lymph node status, TNM stage, tumor location and focus type, were obtained from their medical records.
Cell culture and transfections
BCPAP and TPC-1 cells were cultured in RPMI1640 media (KeyGEN, Nanjing, China) supplemented with 10% fetal bovine serum and penicillin/streptomycin, and cultured at 37 °C in a humidified incubator containing 5% CO2. Transfection was performed following the small-interfering RNA (siRNA) sequences transfection protocol for Lipofectamine RNAi MAX (Invitrogen, USA). Nonsense RNAi (nsRNA) was used as a negative control. Transfection efficiency was evaluated by quantitative real-time RT-PCR and western blot. miR-144 mimic, control mimic, control inhibitor, miR-144 inhibitor and siRNAs against E2F8 were synthesized by Genechem. The sequences used were: siRNA-1 for E2F8: 5’-GGCCAAAGACUGUAUACACTT-3’(sense), 5’-GUGUAUACAGUCUUUGGCCTT-3’(antisense); siRNA-2 for E2F8: 5’-GCCCUAUCAAGACCAACAATT-3’(sense), 5’-UUGUUGGUCUUGAUAGGGCTT-3’(antisense). And the following nonsense siRNA was used as negative control (NC): 5’-UUCUCCGAACGUGUCACGUTT-3’(sense), 5’-ACGUGACACGUUCGGAGAATT-3’(antisense). miR-144 mimic: 5’-UACAGUAUAGAUGAUGUACU-3’. The human E2F8-targeting small hairpin RNA sequences were designed based on siRNA-1 and nsRNA. We generated recombinant lentiviral particles and cells were transfected with E2F8 or negative control recombinant lentivirus (shRNA-E2F8 or shRNA-NC, respectively). For overexpressing miR-144, recombinant lentiviruses containing miR-144 precursor or negative control sequences were purchased from Genechem. For overexpressing CCND1 and E2F8, CCND1 cDNA and E2F8 cDNA without 3’-UTR were cloned into a pEGFP-N1 vector (purchased from Genechem) to construct overexpression plasmid, and an empty vector (EV) was used as a negative control.
Luciferase reporter assay
A wild-type 3’-UTR fragment of E2F8 cDNA was amplified by using PCR and cloned into XbaI and SacI site of pmirGLO dual-luciferase miRNA target expression vector (Promega, Madison, WI, USA) and named as WT-E2F8 3’-UTR. The mutant variant of E2F8 3’-UTR was generated based on WT-E2F8 3’-UTR by mutating six nucleotides that potentially bind to miR-144 and named as Mut-E2F8 3’-UTR. These vectors (WT-E2F8 3’-UTR or Mut-E2F8 3’-UTR were together with miR-144 mimic or miR-NC) were transiently transfected into BCPAP and TPC-1 cells using Lipofectamine 2000 reagent (Invitrogen). Luciferase activity was measured using the Dual-Luciferase Reporter Assay System (Promega, Madison, USA) after transfection at 48 h. Data are presented as the mean value ± SD for triplicate experiments.
RNA extraction and quantitative real-time(qRT)-PCR
Total RNA was extracted from cultured cells using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instruction. The qRT-PCR data collection was performed using a QuantStudioTM 6 Flex Real-Time PCR System and the qRT-PCR reaction included an initial denaturation step at 95 °C for 10 min, followed by 40 cycles of 92 °C for 15 s and 60 °C for 1 min. The primers are shown in Additional file 2: Table S2. Each sample was run in triplicate and the relative expression was calculated and normalized using the 2-ΔΔCt method.
Protein preparation and western blot
Cells were harvested and treated with lysis buffer on ice (KeyGEN, Nanjing, China), and a BCA kit (KeyGEN, Nanjing, China) was used to quantify protein concentration. Equal amounts of protein were loaded in SDS–PAGE gels. After separation in the gel, the protein was transferred on a PVDF membrane. Membranes were blocked in 2% BSA in TBS-T for 1 h, and then incubated overnight (4 °C) with antibodies against E2F8 (Abcam, ab185727 1:1000), cyclin D1 (CST, 2978 1:1000) or β-actin (Cell Signaling, 8H10D10 1:1000). After being washed in TBS-T, membranes were incubated with goat anti-rabbit HRP-conjugated secondary antibody (1:10,000; Abcam) or goat anti-mouse HRP-conjugated secondary antibody (1:10,000; Abcam) for 2 h at room temperature. The blots were visualized by ECL detection (Thermo Scientific). All experiments were repeated at least three times independently.
TMA and immunohistochemistry
A tissue microarray (TMA) containing 58 paired formalin-fixed paraffin-embedded (FFPE) PTC and adjacent normal tissue samples was used. The TMA was purchased from the Shanghai Biochip Co., Ltd., Shanghai, China. All tissues were re-examined by an experienced pathologist after they were transferred from a local hospital and the TNM stage was determined in each patient.
Immunohistochemistry(IHC) for E2F8 protein expression in samples was performed using standard methods. Briefly, tissue sections were deparaffinized and rehydrated through graded alcohol. Endogenous peroxidase activity was blocked by incubation in 3% H2O2. Antigen retrieval was carried out with 0.01 M citrate buffer (pH 6.0) and microwave heat induction. E2F8 staining was scored by blinded observers (including a pathologist) according to intensity and percentage of positive cells. The staining intensity was scored according to 4 grades: 0 (No staining), 1 (weak staining), 2 (intermediate staining), or 3 (strong staining). The product (percentage of positive cells and respective intensity scores) was used as the final staining score (a minimum value of 0 and a maximum of 300).
Cell proliferation assay
The cell proliferation was monitored using a Cell Counting Kit-8 (KeyGEN, Nanjing, China) or the xCELLigence system. After transfection, cells were plated in 96-well plates at a density of 2000 cells in 100ul per well and the absorbance was measured at 450 nm with an ELx-800 Universal Microplate Reader. Experiments were repeated at least three times with similar data. For the xCELLigence system, exponentially growing cells with corresponding treatment in complete media were seeded in E-plates at a density of 20,000 per well. The plates were then locked into the RTCA DP device in the incubator. The proliferative ability in each well was automatically monitored by the xCELLigence system and expressed as a “cell index” value. The cell growth was recorded in real-time for 90 h.
For colony formation assay, a total of 100 transfected cells were placed in a fresh 6-well plate and maintained in media containing 10% FBS, replacing medium every 3 or 4 days. After 2 weeks, cells were fixed with 4% paraformaldehyde and stained with 0.1% crystal violet. Visible colonies were then counted. For each treatment group, each well was assessed in triplicate.
Cell cycle analysis
Flow cytometry analysis was performed to detect cell cycle distribution. Cells were transferred and fixed in centrifuge tubes containing 4.5 mL of 70% ethanol on ice. The cells were kept in ethanol for at least 2 h at 4 °C. Then, the ethanol-suspended cells were centrifuged for 5 min at 300 g. Cell pellets were resuspended in 5 mL of PBS for approximately 30 s and centrifuged at 300 g for 5 min, then resuspended in 1 mL of PI staining solution and kept in the dark at 37 °C for 10 min. Samples were analyzed using a FACSCalibur flow cytometer. The percentage of the cells in G0–G1, S, and G2–M phases were counted and compared. All the samples were assayed in triplicate.
All animal studies were conducted in accordance with NIH animal use guidelines and protocols approved by Nanjing Medical University Animal Care Committee. Twelve male nude mice (ages 4–6 weeks) were purchased from Nanjing Medical University School of Medicine’s accredited animal facility. Briefly, in each group, 1.0 × 106 exponentially growing TPC-1 cells were injected in axilla subcutaneously. Tumor volume was estimated using calipers every week as length × width2 × 0.5. Five weeks after injection, mice were sacrificed, tumor weights were measured and tumors were collected for further analysis.
All statistical analyses were performed using SPSS Statistics (version 20.0, Chicago, Ill) and GraphPad Prism 6 software (GraphPad Software, Inc., La Jolla, CA, USA). The results were presented as mean ± S.D. Relative quantification of mRNA expression level was calculated with the 2-ΔΔCt method. Student’s t-test was used to analyze difference between two groups. Correlation of E2F8 expression with other genes was analyzed using Pearson test. Association of E2F8 expression with clinicopathological parameters was analyzed using Chi-square test. p < 0.05 was considered statistically significant.
Upregulation of E2F8 correlates with more aggressive clinicopathological features in PTC
Correlation between E2F8 expression and clinical characteristics(n = 64)
Age at diagnosis(years)
Lymph node status
To evaluate the protein expression of E2F8 in PTC tissues from a cohort of 58 papillary thyroid cancer patients, immunohistochemistry(IHC) was performed using specific anti-E2F8 antibody. As results, we observed that E2F8 was predominantly localized in the nuclei of PTC cells. Significantly higher expression of E2F8 was observed in PTC tissues compared with matched adjacent normal tissues (staining score: 202.8 ± 6.182 vs 96.90 ± 6.940; p < 0.001) (Fig. 1e and f). Consistent with mRNA results as mentioned above, the score of E2F8 staining was also significantly increased along with more advanced T stage in PTC tissues (Fig. 1e and g).
Knockdown of E2F8 inhibits PTC cells proliferation and induces cell cycle arrest in vitro
Finally, the effect of E2F8 on cell cycle distribution was evaluated by flow-cytometry analysis. As shown in Fig. 2f and g, the percentage of BCPAP and TPC-1 cells transfected with siRNA-E2F8 was significantly increased in G1 phase compared to siRNA-NC.
Silence of E2F8 suppresses tumor growth in vivo
E2F8 exerts its oncogenic activity via influencing CCND1
Considering that knockdown of E2F8 induces G1 phase arrest in vitro, we sought to determine the mRNA levels of CCND1, CCNE1, CCNE2, CDK1, CDK4, CDK6, p21 and p27 which were closely related to G1 phase or G1/S transition in both shRNA-E2F8 or shRNA-NC cells by qRT-PCT. Interestingly, compared with shRNA-NC transfected cells, the result showed that mRNA expression levels of CCND1, CCNE1, CCNE2 and CDK6 were significantly decreased, p21 was significantly increased, while CDK1, CDK4 and p27 were not influenced in shRNA-E2F8 transfected cells (Fig. 4b). Among these genes, considering CCND1 was a key factor to control G1 phase and it was also the most change in mRNA level, we validated its protein level in shRNA-E2F8 cells. By western blot, the data showed that CCND1 expression was markedly decreased in shRNA-E2F8 group compared to shRNA-NC group (Fig. 4c). To examine whether E2F8 regulated the proliferation of TPC-1 cells via altering CCND1, TPC-1 cells with shRNA-E2F8 was transfected with pEGFP-N1-CCND1 plasmid. Transfection efficiency was determined by western blot (Fig. 4e). By the xCELLigence system analysis, the data showed that the proliferation ability was partially recovered in TPC-1 cells with shRNA-E2F8 after enforced overexpression of CCND1(oe-CCND1) (Fig. 4d). Moreover, flow-cytometry analysis showed that oe-CCND1 significantly alleviated shRNA-E2F8-mediated G1-phase arrest of TPC-1 cells (Fig. 4f and g). Our results demonstrated that E2F8 might promote PTC cells proliferation by regulating cell cycle, especially by influencing CCND1.
E2F8 is specifically targeted by miR-144
MiR-144 inhibits proliferation and induces G1 phase arrest in PTC cells
To test whether restoration of E2F8 could reverse miR-144-mediated inhibition of proliferation of PTC cells, we performed the rescue experiments in TPC-1 cells. We found that enforced overexpression of E2F8(oe-E2F8) by transfection of a cDNA that lacked the miR-144-binding site in the 3’-UTR partially abrogated miR-144-mediated suppression of proliferation in TPC-1 cells (Fig. 6g). As shown in Fig. 6h and i, flow-cytometry analysis also showed that oe-E2F8 partially alleviated miR-144-mediated G1-phase arrest. Expression of E2F8 and CCND1 was verified by western blot in each group (Fig. 6j).
MiR-144 inhibits tumor growth in vivo
MiR-144 is downregulated in PTC tissues and inversely correlates with E2F8 expression
Sustaining proliferation is thought to be a fundamental hallmark of cancer . Generally, cell cycle progression is dysregulated in cancer cells, thereby breaking homeostasis of cell number and causing uncontrolled cell proliferation . During cell cycle progression, G1/S transition is thought to be a critical step, in which certain cyclins, cyclin-dependent kinases (CDKs) and cyclin dependent kinase inhibitors participate. For instance, CCND1 binds to CDK4 or CDK6, which in turn phosphorylates Rb to promote G1/S transition .
E2F proteins have been proved to be important regulators in malignant progression in various cancers. Newly identified E2F8 was reported to be a critical proliferation promoter in several human cancers [14–16]. However, the clinical significance and biological function of E2F8 in papillary thyroid cancer remain unknown.
In this study, we present the first evidence that upregulation of E2F8 occurs widely in PTC, and positively correlates with more aggressive clinicopathological features at both mRNA and protein levels. GO enrichment analysis showed that the term “cell cycle” ranks first among E2F8-related potential pathways. Consistent with this finding, experiments in vitro showed that suppression of E2F8 significantly inhibited cell proliferation via G1-phase arrest. We therefore measured several critical G1-phase genes or G1/S transition regulators to explore the potential mechanism. We found that CCND1 was the most decreased one in shRNA-E2F8 cells. Then rescue experiment was performed, and we found that enforced overexpression of CCND1 could greatly increase proliferation ability and alleviate G1-phase arrest in shRNA-E2F8 cells. CCND1 was a well-documented important regulator that promotes G1/S transition and functions as an oncogene involved in many cancers, including PTC [30–32]. We concluded that E2F8 might exert its proliferative role by influencing CCND1 expression to a great degree in PTC progression.
The development of PTC is regarded as a progressive event involving complicated networks of aberrant gene expression and environmental alteration, in which miRNAs play important roles . In a bioinformatics search for potential miRNAs targeting E2F8, we identified miR-144 as the most promising one. Then, miR-144 was proved to be a specific miRNA targeting E2F8 which has not been previously identified. We found that miR-144 inhibited PTC cells proliferation by decreasing E2F8 posttranscriptionally. The levels of E2F8 mRNA exhibited an inverse correlation with the levels of miRNA-144 in 64 PTC tissues. MiR-144 downregulated the expression of E2F8, and resulted in G1-phase arrest in PTC cells. This result was strongly supported by the rescue experiments in which enforced overexpression of E2F8 could partially reverse cell proliferation inhibition and alleviate G1-phase arrest by miR-144. Our data indicated that miR-144 suppressed PTC cell proliferation at least in part through decreasing the posttranscriptional level of E2F8 (Fig. 8d).
In this study, we provide evidence that E2F8 functions as a proliferation-related oncogene in PTC progression. Moreover, miR-144 appears to be a tumor suppressor through direct inhibition of E2F8. Our results suggest that the miR-144/E2F8/CCND1 axis might represent a potential therapeutic strategy for treatment of human PTC.
Papillary thyroid cancer
Quantitative real-time reverse transcription polymerase chain reaction
The Cancer Genome Atlas
The authors would like to thank Xiaoping Zhou (Director of Information Center, W&C Branch Hospital of Jiangsu Province Hospital) for statistics guidance.
This study was supported by the Jiangsu Provincial Program on Basic Research (NO.BK20131441).
Availability of data and materials
The datasets generated during and/or analysed during the current study are available in the [TCGA] repository: (https://genome-cancer.ucsc.edu/proj/site/hgHeatmap/?datasetSearch=TCGA)
The datasets during and/or analysed during the current study available from the corresponding author on reasonable request.
JS, RS, XHM and CS conceived the study. JS and RS performed the experiments. SZ and XNL coordinated the research and analyzed the data. JS and RS wrote the manuscript. SZ, XNL, SL, and HMB supported the experiments and helped to draft the manuscript. XHM and CS provided the financial support. All authors read and approved the final manuscript.
The authors declare that they have no competing interests.
Consent for publication
This study was approved by the Ethics Committee of Cancer Institute of Jiangsu Province. All animal experiments are in accordance with the guidelines of humane use and care of laboratory animals for biomedical research published by National Institutes of Health.
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