Background
Prostate cancer (PCa) is the most common malignancy in males and a major cause of mortality worldwide, causing approximately 1.6 million incident cases and 366,000 deaths each year [
1]. Risk factors for this disease include advancing age, race, genetics, obesity, physical activity, smoking and occupation [
2]. There are multiple management options for men with PCa, such as surgery, radiation, chemotherapy, vaccines, hormonal therapeutics, and bone-targeting agents [
3]. Despite the efficacy these approaches demonstrated, novel means to assess the presence of PCa, monitor its progression and predict its outcome at an early stage in a reliable manner are still required, which necessitate a better understanding of its underlying molecular processes.
Lysine-specific demethylase 5A (KDM5A), known as a histone H3K4 demethylase [
4], has recently become a promising therapeutic target for cancers due to its key roles in important cancer processes including tumorigenesis, metastasis, and drug tolerance [
5]. Cui et al. reported that KDM5A could stimulate pancreatic cancer cell proliferation in vitro and tumor growth in vivo by suppressing the expression of mitochondrial pyruvate carrier 1 (MPC-1) [
6]. KDM5A was also found to be significantly associated with tumor stage progress and metastasis in patients with clear cell renal cell carcinoma [
7]. Upregulated KDM5A has been demonstrated in prostate tissues, but its downstream mechanisms remain enigmatic [
8].
In addition, abnormal expression of microRNAs (miRs or miRNAs) is also implicated in PCa progression. miR-495 has been identified as a tumor suppressor miRNA in PCa owing to its inhibitory effect on Akt and mTOR, thus it further suppressing cancer cell proliferation, migration, and invasion in vitro [
9]. The silico analysis in the present study revealed that miR-495 could directly bind to the mRNA of YTH domain family 2 (YTHDF2), a member of the YTH domain family and the first discovered m6A reader protein, knockdown of which significantly reduces cell proliferation and migration of PCa DU-145 and PC3 cell lines [
10]. Moreover, YTHDF2 showed a regulatory role in mouse neural development by promoting m6A-dependent degradation of neural development-related mRNA targets, including mps one binder kinase activator 3B (MOB3B) [
11]. MOB3B is a member of the MOBs family that is highly conserved in the eukaryotic species and can act as signal transducers in essential intracellular pathways and have diverse cancer-associated cellular functions [
12]. Hence, based on the aforementioned information, we hypothesized that KDM5A could participate in the development of PCa via the miR-495/YTHDF2/m6A-MOB3B signaling axis. We therefore performed in vitro and in vivo experiments to verify the clinical signification of the KDM5A/miR-495/YTHDF2/m6A-MOB3B signaling in the development of PCa.
Materials and methods
Ethics statement
The current study was approved by the Ethics Committee of Harbin Medical University Cancer Hospital and performed in strict accordance with the Declaration of Helsinki. All participants signed informed consent prior to enrollment. Extensive efforts were made to ensure minimal usage of animals as well as their suffering.
Study subjects
A total of 78 patients who received radical prostatectomy and transurethral resection of the prostate at the Department of Urology of Harbin Medical University Cancer Hospital from June 2014 to June 2016 were recruited in our study. None of these patients received anti-tumor treatment before surgery. The cancer tissue samples without necrosis or hemorrhage were biopsied during surgery with adjacent normal tissues (no cancer cells confirmed by pathological examination) and stored in a − 80 °C freezer. The demographic information of patients was extracted and collected from the medical record system, and all patients were followed up post-surgery in order to understand the clinical outcomes after treatment and obtain comprehensive clinical data of patients. The follow-up ended in December 2019, with a total of 3–36 months. Kaplan-Meier method was used to analyze the correlation between KDM5A expression and total survival (OS) and progression-free survival (DFS).
Immunohistochemistry
Paraffin sections of tumor tissues from each group were taken for immunohistochemical analysis, which were dewaxed, dehydrated by alcohol gradient, and immersed in 3% methanol H2O2 for 20 min. Antigen was repaired through water-bath of repair solution. Sections were then blocked with normal goat serum blocking solution (C-0005, Haoran Bio, Shanghai, China) and placed at room temperature for 20 min to dry the slides. Next, sections were incubated with primary antibody to KDM5A (ab92533, 1:500) overnight at 4 °C. The secondary antibody goat anti-rabbit immunoglobulin G (IgG) was then added into the sections and placed at 37 °C for 20 min. After addition of horseradish peroxidase labeled Streptomyces ovalbumin working solution (0343-10,000 U, ImunBio, Beijing, China) the sections were placed at 37 °C for 20 min. Color was developed with diaminobenzidine (DAB; ST033, Whiga Biotechnology, Guangzhou, China) and sections were counterstained with hematoxylin (PT001, Bogoo, Shanghai) for 1 min, turned blue with 1% ammonia water and dehydrated by gradient alcohol. After regular permeabilization and mounting, sections were observed under a microscope with each section randomly selected under five high power field of view. A total of 100 cells were counted in each field. Positive cells < 10% was taken for negative, while positive cells ≥10% and < 50% for positive, and positive cells > 50% was considered as strong positive.
RNA isolation and quantitation
The total RNA was extracted from cancer tissues and cells using the TRIzol reagent (Invitrogen, Carlsbad, CA, USA). The RNA was then reversely transcribed into complementary DNA using the TaqMan MicroRNA Assays Reverse Transcription primer (4,427,975, Applied Biosystems, USA)/PrimeScript RT reagent Kit (RR047A, Takara, Japan). The primers for KDM5A, miR-495, YTHDF2 and MOB3B were designed and synthesized by Takara Holdings Inc. (Kyoto, Japan) (Table
1). Subsequently, reverse transcription quantitative polymerase chain reaction (RT-qPCR) was conducted on an ABI 7500 instrument (Applied Biosystems, Foster City, CA, USA). The fold changes were calculated using the 2
-ΔΔCt method with U6 and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) serving as internal references, respectively.
Table 1
Primer sequences for RT-qPCR
KDM5A | Forward: 5′-TTACCAACAGGTCAGACGCAT-3′ |
Reverse: 5′-GGTTTGCTACATTCCTCGGCG-3′ |
miR-495 | Forward: 5′-GGGGAAACAAACATGGTGCAC-3′ |
Reverse: 5′-CAGTGCGTGTCGTGGAGT-3′ |
YTHDF2 | Forward: 5′-CATGAATGGGAAGGGTCCCG-3′ |
Reverse: 5′-GACGAATGTGTCGCAGTTGG-3′ |
MOB3B | Forward: 5′-GTGGCAGGATGATCTCAA-3′ |
Reverse: 5′-CGGCACAGGATCTTCTTG-3′ |
U6 | Forward: 5′-CTCGCTTCGGCAGCACA-3′ |
Reverse: 5′-AACGCTTCACGAATTTGCGT-3′ |
GAPDH | Forward: 5′-CTGGGCTACACTGAGCACC-3′ |
Reverse: 5′-AAGTGGTCGTTGAGGGCAATG-3′ |
Western blot analysis
Total protein was extracted from cancer cells and tissues using radio-immunoprecipitation assay lysis buffer, with the protein concentration then determined with a bicinchoninic acid kit. The protein was separated and transferred onto a polyvinylidene fluoride membrane. The membrane was then blocked and underwent overnight incubation with primary antibodies against KDM5A (1:10000), H3K4me3 (1 μg/mL, rabbit, Abcam, USA), YTHDF2 (1:2000, rabbit) and MOB3B (1:1000, rabbit, Sigma-Aldrich Chemical Company, St Louis, MO, USA). The next day, the membrane was re-probed with horseradish peroxidase-labeled secondary goat anti-rabbit IgG (1:1000, Santa Cruz Biotechnology, Inc., Santa Cruz, CA, USA). Afterwards, the membrane was visualized and the protein bands were quantified using the Bio-Rad ChemiDoc™ system and ImageJ2x software. The ratio of the gray value of the target band to GAPDH (1:10000, rabbit, Santa Cruz Biotechnology, Inc., Santa Cruz, CA, USA) was representative of the relative protein expression.
Cell culture and transfection
PCa cell lines (LNCaP, C42, DU145 and PC3) were purchased from American Type Culture Collection (ATCC; Manassas, VA, USA). The normal human prostate epithelial cell line RWPE-1 (Oulu Biotechnology, Shanghai, China) served as a control, and were cultured in Roswell Park Memorial Institute (RPMI) 1640 medium (Gibco, USA) containing 10% fetal bovine serum (Gibco, USA), 100 μg/mL streptomycin and 100 U/mL penicillin in a 5% CO2 incubator (Thermo Fisher Scientific Inc., Waltham, MA, USA) at 37 °C. Upon reaching approximately 75% confluence, the cells were transiently transfected using Lipofectamine 2000 (Invitrogen) with the following plasmids purchased from Sino Biological, Inc. (Beijing, China): overexpression (oe)-KDM5A, short hairpin RNA (sh)-KDM5A (sh1-KDM5A [5′-GGAACUGGGUCUCUUUUGA-3′], sh2-KDM5A [5′-GCAAAUGAGACAACGGAAA-3′] and sh3-KDM5A [5′-UGACAAUGGUGGACCGCAU-3′]), oe-KDM5A + miR-495 mimic, miR-495 mimic, miR-495 inhibitor, miR-495 mimic + oe-YTHDF2 and oe-KDM5A + oe-MOB3B as well as their corresponding controls (oe-negative control [NC], sh-NC, oe-NC + mimic NC, oe-KDM5A + mimic NC, mimic NC, inhibitor NC, mimic NC + oe-NC, miR-495 mimic + oe-NC, mimic NC + oe-YTHDF2 and oe-KDM5A + oe-NC). After 6 h of transfection, the cells were cultured for 48 h and then collected.
PCa cells were inoculated into dishes containing 10 mL preheated culture medium, and evenly dispersed by gentle rotation, followed by culture, with the culture medium changed once every 2–3 days. The culture was halted once the clone in the dish was visible to the naked eyes. After removal of supernatant, the cells were washed, and fixed. The fixed cells were stained with an appropriate amount of GIMSA (Invitrogen, USA) for 10–30 min. The number of cell clones was counted under an inverted microscope (Leica DMi8-M, Co. Ltd., Solms, Germany), and the colony formation rate was calculated using the formula: the number of cell clones/the number of inoculated cells × 100%.
Flow cytometry
Annexin V-fluorescein isothiocyanate (FITC)/propidium iodide (PI) double staining method was used to detect cell apoptosis. The PCa cells were inoculated into 6-well plates at a density of 2 × 105 cells/well. After cell transfection, the culture medium was removed, and the cells were trypsinized and collected in a centrifuge tube for centrifugation at 800 g, with the supernatant discarded. According to the instructions of the Annexin V-FITC Apoptosis Detection Kit (BD Biosciences, San Jose, CA, USA), the cells were resuspended, and added with 5 μL FITC and 5 μL PI under dark conditions. At last, the cell apoptosis was detected using BD FACSCalibur.
Transwell assay
PCa cells were starved, then digested, and resuspended in serum-free Opti-MEMI medium (Invitrogen, USA). The cell suspension was then seeded into the 8-μm Transwell chamber (Corning, NY, USA) in a 24-well plate (100 μL per chamber, a total of 3 chambers). Next, 600 μL 10% RPMI-1640 medium was added to the lower chamber and incubated. For the cell migration experiment, the cells were fixed, after which the chamber was treated with 0.2% Triton X-100 solution (Sigma-Aldrich Chemical Company, St Louis, MO, USA), and stained with crystal violet.
During cell invasion experiment, 50 μL Matrigel (Sigma-Aldrich Chemical Company, St Louis, MO, USA) settled in the chamber before the experiment. After 48 h, fixation and staining were conducted with the aforementioned procedures. The number of stained cells was counted in five randomly selected visual fields under an inverted microscope (Leica DMi8-M, Co. Ltd., Solms, Germany) to obtain the mean value.
Scratch test
After 48 h of transfection, PCa cells were seeded into 6-well plates at a density of 5 × 105 cells/well. After the cells completely adhered to the bottom, a scratch was made in the middle of each well using a 2-mm cell scraper and the cell culture was continued for 24 h. The cells were photographed at 0 h and 24 h after scratch, and the rate of scratch healing was calculated with the Image-Pro Plus 6.0 software (Media Cybernetics, Inc., Silver Spring, MD, USA).
Dual luciferase reporter assay
The predicted binding site and mutation fragments of miR-495 promoter with KDM5A were inserted into luciferase reporter vectors (Beijing Huayueyang Biotechnology Co., Ltd., Beijing, China), known as reporter plasmids miR-495 promoter-wild-type (WT) (with sequence of 3′-CAGTGACCCA-5′) and miR-495 promoter-mutant (MUT) (with sequence of 3′-TGAGAGTATG-5′). Oe-NC and oe-KDM5A were co-transfected into 293 T cells (Oulu Biotechnology, China) with miR-495-WT and miR-495-MUT plasmids in order to detect whether KDM5A could bind with KDM5A. After 48 h of transfection, cells were collected and lysed. The luciferase activity was detected with the use of a luciferase assay kit (K801–200, Biovision, Bay Area, San Francisco, USA) on the analysis system (Promega Corporation, Madison, WI, USA). With renilla luciferase as a loading control, the luciferase activity was calculated as the relative luciferase unit (RLU) activity of firefly luciferase/RLU activity of renilla luciferase. Likewise, the interaction between miR-495 and YTHDF2 was detected in the same way.
Chromatin immunoprecipitation (ChIP) assay
After 48 h of transfection, PCa cells from each group were fixed in 1% formaldehyde at 37 °C for 10 min, which was then terminated by adding glycine solution for a 5 min reaction on ice. After rinsing with PBS, the cells were incubated and centrifuged to obtain cell precipitate. The cells were resuspended in 200 μL SDS lysis buffer for 10 min on ice. The chromatin DNA was broken by ultrasound on ice. The cells were centrifuged at 14000 rpm for 10 min, after which the supernatant was diluted with ChIP buffer containing protease inhibitor, and with blocking solution added for a 30-min incubation at 4 °C. After centrifugation at 1000 rpm for 1 min, the supernatant was collected and divided into three parts, with one as Input, one being incubated with rabbit IgG antibody (Abcam, China) as the NC, and the other part incubated with rabbit KDM5A antibody (2 μg used for 25 μg of chromatin, Abcam, China) at 4 °C overnight. We added Protein G Dynabeads (Thermo Fisher Scientific Inc., Waltham, MA, USA) to the supernatant and incubated it at 4 °C for 1 h to precipitate antibody-transcription factor complex. After centrifugation at 1000 rpm for 1 min, the precipitate was washed and eluted with elution buffer. Twenty μL NaCl (5 mol/L) were added into the eluted precipitate and Input DNA respectively and bathed in water at 65 °C for 4 h to ravel the DNA cross-linking. DNA fragments were then purified and recovered post-incubation with protease K. Subsequently, RT-qPCR was conducted to detect the expression of miR-495 with the recovered DNA as a template.
Methylated RNA binding protein immunoprecipitation (me-RIP) assay
Total RNA was extracted from tissues and cells using the TRIzol method. The mRNA in the total RNA was isolated and purified using the PolyATtract® mRNA Isolation Systems (A-Z5300, A&D Technology Corporation, Beijing, China). IP buffer supplemented with 20 mM Tris pH 7.5, 140 mM NaCl, 1% NP-40 and 2 mM EDTA was added m6A antibody (1:500, ab151230, Abcam, USA) or IgG antibody (ab109489, 1:100, Abcam, USA) and incubated with protein A/G magnetic beads for 1 h in order for binding. IP buffer with ribonuclease inhibitor and protease inhibitor was then added with the purified mRNA-bead-antibody complex and incubated overnight at 4 °C. The RNA was eluted with elution buffer, and purified with phenol-chloroform. MOB3B was analyzed by RT-qPCR.
Photo-activatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP)
PCa tissues and cells were incubated with 200 mm 4-thiopyridine (Sigma, USA) for 14 h, and cross-linked with 0.4 J/cm2 at 365 nm. After cleavage, YTHDF2 antibody (5 mg and 3 mg respectively) was used for immunoprecipitation at 4 °C. The precipitated RNA was then labeled with [g-32-P]-ATP and observed by autoradiography. After protease K treatment, the RNA was extracted and MOB3B expression was detected by RT-qPCR.
Xenograft tumor in nude mice
A total of 36 specific pathogen-free male Balb/c mice (aged 5 weeks; weighing 18–22 g) were purchased from Shanghai SLAC Laboratory Animal Co., Ltd. (Shanghai, China). PCa cells were resuspended in serum-free RPMI-1640 medium (Gibco, USA) to cell suspension at a density of 1 × 106 cells/200 μL. The Balb/c nude mice were randomly divided into three groups (n = 12 in each group), and the tumorigenesis experiment lasted for 4 weeks. Under anesthesia with ether, the nude mice were disinfected and subcutaneously inoculated with cells transfected with oe-NC, oe-KDM5A + oe-NC and oe-KDM5A + oe-MOB3B at a density of 1 × 106 cells/mouse (200 μL) at the back of the right hind leg. All nude mice were raised in the same environment, with themselves and their inoculation site being observed every day. The tumor size was measured every 7 days, and the length and width of the tumor were recorded, with the tumor volume estimated as length × width2/2. After 4 weeks, all mice were euthanized by cervical dislocation under anesthesia, and their tumor tissue was dissected, photographed and weighed.
Statistical analysis
All data were processed using the SPSS 21.0 (IBM Corp. Armonk, NY, USA) with a level of p < 0.05 as statistical significance. Continuous data were demonstrated as mean ± standard deviation. Data with normal distribution and homogeneity of variance between two groups were compared using t-test. Comparison of the mean among multiple groups were analyzed by one-way analysis of variance (ANOVA) with Tukey’s post hoc test or repeated measures ANOVA with Bonferroni post hoc test. Kaplan-Meier method was used to calculate the survival rate and duration of the patients, with Log-rank test used for single factor analysis. Pearson correlation coefficient was utilized for correlation analysis.
Discussion
Histone lysine demethylases have emerged as novel prognostic factors and therapeutic targets for prophylaxis and management of advanced PCa [
13]. In the present study, we investigated the cancer-promoting mechanism of KDM5A underlying the pathogenesis of PCa. The obtained in vitro and in vivo experimental results demonstrated that KDM5A elicited PCa progression via downregulation of miR-495 expression and YTHDF2-mediated MOB3B inhibition.
KDM5A gene is significantly amplified and overexpressed in various human cancers, such as ovarian cancer, small cell lung cancer and breast cancer [
4,
14,
15]. In the present study, KDM5A was found to be expressed at high levels in human PCa tissues and cell lines. Similarly, Vieira group found that the upregulated KDM5A expression in PCa tissues compared with normal prostate tissues, but its downstream mechanism has not been fully elucidated [
8]. Our study showed that upregulated KDM5A could promote proliferation, migration and invasion of PCa cells while reducing cell apoptosis via the inhibition of miR-495. It has been reported that KDM5A downregulates miR-21 expression in leukemia cells by directly binding to the promoter sequence of miR-21 and demethylating trimethylated H3K4 at the miR-21 locus [
16]. Consistent with our findings, ChIP-seq data revealed that KDM5A could bind to the promoter of miR-495 and consequently repress its expression.
Accumulating evidence has identified miR-495 to be a tumor suppressor miRNA in PCa. miR-495 is decreased in PCa cell lines compared with normal prostatic epithelial cells [
17]. Moreover, amplified miR-495 has been found to inhibit PCa cell proliferation, migration, and invasion in vitro as well as significantly retarding the growth of tumors in vivo by repressing its targets Akt and mechanistic target of rapamycin (mTOR) [
9]. miRNAs can modulate gene expression posttranscriptionally by interacting with the 3′-untranslated region (UTR) of specific target mRNAs [
18]. In the present study, we confirmed that YTHDF2 is a target gene of miR-495 and could be negatively regulated by it. Chen et al. found that mRNA and protein expression of YTHDF2 is upregulated in PCa tissues compared with adjacent normal tissues, which can promote cell proliferation of prostate tissues [
19]. Recent evidence demonstrates that miRNAs play an important role in regulation of cancer cell growth, invasion and metastasis through suppression of the expression of their target genes [
20]. Those findings thus supported our conclusion that upregulated YTHDF2 abolished the inhibitory effects of miR-495 on PCa cell functions of proliferation, invasion and migration and the inducing effects on cell apoptosis.
The m6A reader protein YTHDF2 has been previous reported to promote mRNA degradation by recognizing m6A and recruiting the mRNA decay machinery [
11]. More specifically, following the binding of YTHDF2 to m6A sites, the recognized mRNAs are degraded and m6A levels are decreased accordingly [
10]. The findings from our present study revealed that YTHDF2 might recognize m6A modification of MOB3B mRNA and then enhance the mRNA degradation, ultimately disrupting the expression of MOB3B. In accordance to our results, the mRNA expression of MOB3B is significantly lower in PCa tissues than in healthy control tissues, which is further closely associated with aggressive pathophysiological features in patients with PCa [
21]. By directly binding to the promoter region of MOB1, KDM2B has been demonstrated to suppress the promoter activity of MOB1 and transcriptionally inhibit MOB1 expression, thus augmenting the proliferation, migration and invasion of pancreatic ductal adenocarcinoma cells [
22], which is partially in consistent with our results. Furthermore, in the response of both PC3 cell line and nude mice to KDM5A overexpression, the mRNA and protein levels of YTHDF2 was found to be significantly downregulated. We concluded that KDM5A stimulated PCa initiation by downregulating MOB3B expression via regulation of the miR-495/YTHDF2 axis both in vivo and in vitro. However, limitation exists. it will be good to compare PC3 cells with other PCa cells, such as LNCaP and DU145 cells in future studies, so as to validate the effects in PCa cells with different metastatic potential and different survival and proliferation characteristics. Moreover, the in vitro findings could also be verified with future confirmatory experiments in normal prostate epithelial cells.
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