Introduction
Bladder cancer (BCA) has become the fifth most common cancer in USA, with 81,190 estimated new cases in 2018 [
1]. The development of bladder cancer is a complex process, which is caused by abnormal genetic changes and/or epigenetic abnormalities. Epigenetic abnormalities mainly occur in many levels including DNA [
2], RNA [
3] and histone modification [
4‐
7]. In RNA levels, more than 100 types of post-transcriptional modifications have been identified. Among them, N6-methyladenosine (m6A) RNA methylation is one of the most common modifications, accounting for about 50% of total methylated ribonucleotides and 0.1–0.4% of all adenosines in total cellular RNAs [
8,
9]. In bladder cancer, Cheng.et al has verified that the m6A level in tumor tissues was significantly elevated. They further found that methyltransferase-like 3 (METTL3), an main component in the so-called m6A ‘writer’, could promote bladder cancer progression via AFF4/NF-κB/MYC signaling network by an m6A dependent manner [
10].
METTL3 is known to be involved in all stages in the life cycle of RNA. It plays a pivotal role in pre-mRNA splicing [
11,
12], 3′-end processing [
13,
14], nuclear export [
15‐
17], translation regulation [
18,
19], messenger RNA (mRNA) decay [
20‐
22], and microRNA (miRNA) processing [
23,
24]. Accordingly, METTL3 affects the tumor formation by the regulation the m6A modification in the mRNAs of critical oncogenes or tumor suppressors [
25‐
28]. At the level of non-coding RNAs, METLL3 could promote the formation of m6A-circRNAs, exhibiting distinct patterns of m6A modifications compared to mRNAs [
29] . Moreover, it could affect the internal m6A modification of lincRNA1281 and mediate a competing endogenous RNA (ceRNA) model to regulate mouse embryonic stem cell differentiation [
30].Alarcon et al found that METTL3 could promote the maturation of miRNAs (let-7e, miR221/222, miR4485, miR25, miR93, miR126 and miR335 et al) by interact with the microprocessor protein DGCR8 [
24]. These suggested that METLL3 could exhibit its roles in normal human physiological process or diseases by regulating the m6A modification of the non-coding RNAs. However, whether this mechanism is related to the proliferation of tumors induced by METTL3 is not reported yet.
In the present study, we indeed found METTL3 exhibited its oncogenic role in bladder cancer through interacting with the microprocessor protein DGCR8 and positively modulating the pri-miR221/222 process in an m6A-dependent manner. Moreover, high expression of METTL3 was related to poor prognosis in bladder cancer patients. It implies that METTL3 may serve as a novel prognostic and/or therapeutically target in bladder cancer.
Materials and methods
Clinical specimens
Bladder cancer tissues and their paired normal tissues were obtained from patients who were diagnosed with bladder cancer and undergone surgery in the First Affiliated Hospital with Nanjing Medical University (Jiangsu Province Hospital) between 2010 and 2013. The follow-up deadline was January 2018. All patients signed informed consent before using clinical materials. The use of tissues for this study has been proved by the ethics committee of the First Affiliated Hospital with Nanjing Medical University (Jiangsu Province Hospital).
Cell culture
The bladder cancer cell lines EJ and T24 were obtained from the Type Culture Collection of the Chinese Academy of Sciences (Shanghai, China). All cells were cultured in DMEM medium containing 10% fetal bovine serum (FBS; Gibco, Australia) and 1% penicillin–streptomycin with 5% CO2 at 37 °C in a humidified incubator.
Transfection
The lentivirus constructing of METTL3 knockdown or overexpress was obtained from OBIO (Obio Technology Corp, China). Bladder cancer cells were plated in 6 wells dishes at 50% confluence and infected with METTL3 overexpression lentivirus (termed as oeMETTL3), a negative control (termed as NC), METTL3 knockdown lentivirus (termed as shMETTL3–1, shMETTL3–2), or a scramble control (termed as shNC) in T24 and EJ cells, respectively. Pools of stable transductions were generated by selection using puromycin (4 μg/ml) for 2 weeks.
All miRNA mimics used for transfection were purchased from GenePharma (Shanghai, China). Transfections were performed using the Lipofectamine 2000 kit (Invitrogen, USA) according to the manufacturer’s instructions.
Tissue microarray (TMA) and immunohistochemistry (IHC)
TMA (16 × 10) was constructed from 180 cases of formalin-fixed, paraffin-embedded bladder cancer tissues. IHC was performed on TMA to evaluate METTL3 protein expression. TMAs were treated with xylene and 100% ethanol, followed by decreased concentrations of ethanol. After antigen retrieval, TMAs were blocked and stained with anti-METTL3 antibody (1:200, Abcam, USA), followed by secondary antibody incubation and standard avidin biotinylated peroxidase complex method. Hematoxylin was used for counterstaining, and images were obtained with an upright microscope system (Nikon, JAPAN). The total METTL3 immunostaining score was calculated as the sum of the score for the proportion of positively stained tumor cells (PP) and the score for staining intensity (SI) given by two pathologists blinded to the clinical parameters. PP was scored into four categories: 0 (< 5%, negative), 1 (5–25%, sporadic), 2 (25–50%, focal), 3 (> 51%, diffuse) and SI was scored on a scale of 0 to 3 (0, negative staining; 1, weak staining; 2, moderate staining; 3, strong staining). The final staining score was calculated by multiplying SI and PP score, resulting in a score value ranging from 0 to 9. The positive level of IHC staining was scored by two urologists and patients with different scores were divided into low- (0–3) and high-staining (4–9) groups. All information of patients was supplied in Additional file
1: Table S1
RNA extraction and quantitative real-time PCR (qRT-PCR)
Total RNA was isolated from tissues and cells by using Trizol reagent (Invitrogen, USA) according to the manufacturer’s protocol. cDNA was synthesized using HiScript II (Vazyme, China) and qRT-PCR for mRNA and miRNA was performed on StepOne Plus Real-Time PCR system (Applied Biosystems, USA) or LightCycler 480 (Roche, USA). U6 and β-actin were used as an internal standard control for miRNA and mRNA detection, respectively. Each sample was replicated three times and data was analyzed by comparing Ct values. All PCR primers were purchased from GeneCopoeia (Guangzhou, China)and listed in Additional file
2: Table S2.
Western blot
Total cellular proteins were lysed by RIPA buffer containing protease inhibitors (Sigma, USA). The protein extractions were harvested and quantified by bicinchoninic acid (BCA) analysis (Beyotime, China). Protein extractions were separated by 10% SDS-PAGE and transferred onto polyvinylidene fluoride (PVDF) membranes (Millipore, USA). After the incubation with a high affinity anti-METTL3 antibody (1:1000, Abcam, USA), anti-DGCR8 antibody (1:1000, Abcam, USA), anti-PTEN antibody (1:1000, Abcam, USA), anti-β-actin antibody (1:1000, Cell Signaling Technology, USA) or anti-GAPDH antibody (1:1000, Cell Signaling Technology, USA), the membranes were then incubated with peroxidase (HRP)-conjugated secondary antibody (1:1000, Cell Signaling Technology, USA). After washes, signals were detected using a chemiluminescence system (Bio-Rad, USA) and analyzed using Image Lab Software.
Cell proliferation and colony formation assay
For cell proliferation assay, the transfected cells were seeded into 96-well plates at a density of 2000 cells per well. At 0, 24, 48, 72 and 96 h after seeding, cell viability was measured by the cell counting kit-8 (CCK-8) system (Dojindo, Japan) according to the manufacturer’s instructions. Briefly, each well was added with 10 μl CCK-8 solution and the plate was incubated at 37 °C for 1 h in dark. The absorbance was measured at 450 nm with a microplate reader (Tecan, Switzerland).
For colony formation assay, the transfected cells were seeded into 6-well plates at a density of 700 cells per well and maintained in DMEM medium containing 10% FBS for 2 weeks. After fixed with methanol, the cells were stained with 0.1% crystal violet 30 min and then the colonies were imaged and counted.
Cell cycle assay
1 × 106 cells were collected, washed with phosphate buffer saline (PBS) and fixed with 75% cold ethanol for 24 h at − 20 °C. After washed with PBS twice and stained with propidium iodide by the cycletest plus DNA reagent kit (BD Biosciences, USA) at room temperature for 30 min, cells were assessed by flow cytometry (Becton Dickinson, USA) and cell cycle would be analyzed by Cell Quest Modfit software.
RNA m6A dot blot assays
The Poly(A) + RNAs were firstly denatured by heating at 65 °C for 5 min and transferred onto a nitrocellulose membrane (Amersham, GE Healthcare, USA) with a Bio-Dot apparatus (Bio-Rad, USA). The membranes were then UV cross-linked, blocked, incubated with m6A antibody (1:1000, Abcam, USA) overnight at 4 °C and subsequently incubated with HRP-conjugated goat anti-mouse IgG (1:3000, Proteintech, USA). Finally, the membrane can be visualized by the chemiluminescence system (Bio-Rad, USA). The membrane stained with 0.02% methylene blue (MB) in 0.3 M sodium acetate (pH 5.2), was used to ensure consistency among different groups.
Dual-luciferase reporter assay
Cells were co-transfected with plasmids containing 3′-UTR of wild or mutant fragments from PTEN (gene of phosphate and tension homology deleted on chromsome ten) and miRNA mimics using Lipofectamine 3000 (Invitrogen, Foster city, CA) according to the manufacturer’s protocol. At 24 h after transfection, firefly and renilla luciferase activities were measured consecutively by using dualluciferase reporter assay system (Promega, Massachusetts, USA). Finally, ratios of luminescence from firefly to renilla luciferase were calculated.
m6A RNA immunoprecipitation assay (MeRIP)
T24 cells stably transfected with either the METTL3 overexpress lentiviral or control were UV-irradiated at 254 nm, 400 mJ/cm2 (Stratagene Stratalinker), and lysed with RIP lysis buffer (Magna RIP Kit, Millipore, MA) at 4 °C via disruptive sonication. Immunoprecipitations of endogenous DGCR8 were performed using an anti-DGCR8 antibody (1:1000, Abcam, USA) overnight at 4 °C. After washing, the immunoprecipitated protein-RNA complex was analyzed by western blot and treated with Proteinase K. RNAs were extracted by phenol: chloroform: isoamyl alcohol and subjected to qRT-PCR using primers for pri-miRNAs and normalizing to input.
For the m6A RNA binding experiments, the RNAs of T24 cells stably transfected with either the METTL3 overexpress lentiviral or control were isolated and treated with DNase I (Sigma Aldrich, USA). RNAs were fragmented by sonication for 10 s on an ice water mixture. Immunoprecipitations were performed using an anti-m6A antibody (1:1000, Abcam, USA) previously bound to magnetic Dynabeads (Life Technologies, USA) in the RIP Immunoprecipitation buffer (Magna RIP Kit, Millipore, MA) and incubated with DNA-free fragmented RNAs. Beads were then treated with Proteinase K (20 mg/ml) for 1.5 h at 42 °C. RNAs was extracted by phenol: chloroform: isoamyl alcohol and subjected to qRT-PCR using primers for pri-miRNAs and normalizing to input.
Co-immunoprecipitations assay
Co-immunoprecipitation was performed in T24 cells using PierceTM Co-Immunoprecipitation Kit (ThermoFisher Scientific, USA) according to the manufacturer’s protocol. Briefly, immunoprecipitations of METTL3 were performed using an anti-METTL3 antibody (1:1000. Abcam, USA) overnight at 4 °C. After washing, the immunoprecipitated complex was treated with either RNase A or RNase inhibitor (Sigma Aldrich, USA) 5 min at 37 °C. Then anti-DGCR8 (1:1000, Abcam, USA) was used for western blot analysis.
Xenografts in mice
The T24 cells were stably transfected with shMETTL3, oeMETTL3 or their negative control. About 1× 107 cells were injected subcutaneously into the axilla of the female athymic BALB/C nude mice (4–6 weeks old, 18–22 g, five mice per group). Tumor growth was monitored every week by measuring the width (W) and length (L) with calipers, and the volume (V) of the tumor was calculated using the formula V = (W2 × L)/2. Four weeks after injection, the mice were euthanized and tumors were removed, weighed, fixed, and embedded for IHC. The animal studies were performed in accordance with the institutional ethics guidelines for animal experiments, which was approved by the animal management committee of Nanjing Medical University.
Statistical analysis
Data were analyzed using SPSS version 19.0 and presented as means ± standard deviation (SD). Student’s t-test was performed to analyze differences between the two groups, and P < 0.05 was considered to indicate statistical significance. All experiments were repeated more than three times, and each experiment was performed in triplicate.
Discussion
As a main component in the so-called m6A ‘writer’, METTL3 was reported to have the ability to promote bladder cancer progression via AFF4/NF-κB/MYC signaling network by an m6A dependent manner [
10]. In the present study, we found METTL3 promoted bladder cancer proliferation by accelerating the maturation of pri-miR221/222 by an m6A dependent manner, resulting in the reduction of PTEN. To our knowledge, this is the first comprehensive study that METTL3 affected the tumor formation by the regulation the m6A modification in non-coding RNAs.
METTL3 was found to be upregulated in bladder cancer tissues and cell lines significantly. Cheng et al. previously found that METTL3 could promote the proliferation of bladder cancer cell lines 5637 and SV-HUC-1 [
10]. In our study, we firstly verified the expression of METTL3 in six bladder cancer cell lines (EJ, T24, J82, 5637, 253 J, RT4). Then we found that METTL3 was significantly upregulated in bladder cancer cell lines, especially in EJ and T24 cell lines. As METTL3 acted as an oncogene in bladder cancer, we selected T24 and EJ cell lines with higher METTL3 expression for our follow-up experiments. Knockdown of METTL3 significantly inhibited the proliferation of T24 and EJ cell lines, whereas overexpression of METTL3 promoted the proliferation of T24 and EJ cell lines. Similarly, in vivo experiments showed that knockdown of METTL3 in T24 cells formed smaller tumors in nude mice than in the control group, while overexpression of METTL3 in T24 cells formed larger tumors in nude mice. These results confirmed the previous report that METTL3 plays an oncogenic role in bladder cancer. More importantly, we found that METTL3 expression was associated with the histological grade in bladder cancer patients. In addition, the prognosis of bladder cancer patients with high expression of METTL3 was worse, suggesting that METTL3 was a predictor of the prognosis for bladder cancer patients.
Cheng et al. found that METTL3 promoted bladder cancer progression via AFF4/NF-κB/MYC signaling network by an m6A dependent manner. In the present study, we found that METTL3 was required for the engagement of pri-miRNAs by the DGCR8 in bladder cancer. Alarcon. et al reported that METTL3 could promote the maturation of miRNAs, including let-7e, miR221/222, miR4485, miR25, miR93, miR126 and miR335 [
24]. Then, we validated the above-mentioned miRNAs in T24 cell and we found that miRNAs (let-7e, miR221/222, miR4485, miR25, miR93) were significantly altered by METTL3. However, miR126 and miR335 did not change significantly, possibly due to their low levels in bladder cancer cell. Then, we predicted the prognosis of these miRNAs in bladder cancer in the database (
http://kmplot.com/analysis/) and found that only miR221/222 played an oncogenic role in bladder cancer. Then, we verified the expression of miR221/222 and pri-miR221/222 in the METTL3 knockdown and overexpression bladder cancer cells. As expected, knockdown METLL3 increased the expression of pri-miR221/222, while decreased the expression of miR221/222, significantly. While, overexpression METTL3 gave the opposite result. We also found that METTL3 and miR221/222 were positively correlated in bladder cancer patients’ tissues. Moreover, METTL3 could interact with the microprocessor protein DGCR8 and positively modulating the pri-miR221/222 process in an m6A-dependent manner by further immunoprecipitated and MeRIP assay. When we transfected miR221/222 mimics or inhibitors into METTL3 knockdown and overexpression bladder cancer cells, respectively, we found that miR221/222 interference could rescue the proliferation induced by METTL3 in bladder cancer cells. All the results implied that METTL3 could promote the maturation of pri-miR221/222 in bladder cancer by m6A dependent manner.
miRNAs are small non-coding RNAs that perform biological functions by inducing degradation of mRNA targets or blocking translation to inhibit gene expression [
31]. Because of the structural and functional similarities between miR221 and miR222, they are often studied together as miR221/222. miR221/222 has been reported to play an important role in the occurrence and development of many cancers such as bladder cancer [
32], gastric cancer [
33], breast cancer [
34], thyroid cancer [
35], prostate cancer [
36], and so on [
37,
38]. MiR221/222 are crucial molecules targeting anti-oncogenes (including p27, p57 and PTEN) in multiple cancers [
32‐
38]. Garofalo M et al. reported that 3’UTRs of human PTEN (nucleotides 200–207; NM_000314) and human TIMP3 (nucleotides 2443–2449; NM_000362) contained regions that matched the seed sequences of miR-221 and miR-222 by bioinformatics search (Targetscan, Pictar, RNhybrid) [
39]. PTEN was validated to be key molecules in regulating bladder cancer. The loss of PTEN is associated with adverse prognosis, which is expected to be crucial therapeutic target for bladder cancer [
40,
41]. Additionally, early studies demonstrated that multiple oncogenic miRNAs promoted malignancy in tumors by neutralizing PTEN expression [
42]. The combination of miR221/222 and PTEN has also been reported in liver cancer [
39], lung cancer [
39], gastric cancer [
43] and thyroid cancer [
35]. In the present study, the luciferase reporter assay confirmed that miR221/222 could bind to 3′-UTR of PTEN mRNA in bladder cancer. Further functional studies also verified that miR221/222 promoted tumor progression by directly targeting PTEN in bladder cancer. Therefore, we presented PTEN as a targeted gene by miR221/miR222 in bladder cancer.
Vu LP. et al have reported that METTL3 can directly regulate PTEN mRNA in the human acute myeloid leukemia MOLM-13 cell line [
25]. In my study, we mutated the binding site of the 3′-UTR region of PTEN for luciferase reporter assay and m6A RNA immunoprecipitation. Results suggested that METTL3 may not directly regulate PTEN mRNA in bladder cancer. Furthermore, we found that METTL3 and PTEN were negative correlated in bladder cancer patients’ tissues. In bladder cancer cells, we also found that the expression of PTEN was significantly higher in METTL3 knockdown cells, while the expression of PTEN was decreased in METTL3 overexpression cells by qRT-PCR and western blot. Therefore, METTL3 promote the maturation of miR221/222 which could target PTEN, leading to the decrease of PTEN mRNA expression, and ultimately the decrease of PTEN protein expression.
In summary, our results showed that METTL3 was significantly increased in bladder cancer and correlated with poor prognosis of bladder cancer patients. Moreover, METTL3 could promote cell proliferation both in vitro and tumorigenesis in vivo. And we demonstrated that METTL3 could downregulate PTEN expression by interacting with the microprocessor protein DGCR8 and positively modulating the pri-miR221/222 process in an m6A-dependent manner, which may provide a prognostic and/or therapeutically target for the treatment of bladder cancer.
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