Cell lines and cell culture
The human PCa cell lines PC3, DU145, C4-2B, LNCAP and the murine leukemic monocyte macrophage cell line RAW264.7 cells were purchased from the American Type Culture Collection (ATCC, Manassas, USA). Benign prostatic hyperplasia cell line BPH1 was purchased from the Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ, German). PC3, DU145, C42-B, LNCAP and BPH1 cells were cultured in DMEM or RPMI-1640 medium (Thermo Fisher Scientific, MD, USA) containing 10% fetal bovine serum (FBS; Gibco). Raw264.7 was cultured in alpha-MEM (Gibco) with 10% FBS.
Plasmid construction
The firefly luciferase expressional vector phE-luc [12] was employed as a backbone for dual-luciferase report assay. Wide type (WT) and mutant (MUT) sequences of putative microRNA-378a-3p target site(s) on 3’UTR of MAOA and Dyrk1a (named as MAOA-WT,MAOA-MUT, Dyrk1a-T1WT, Dyrk1a-T1MUT, Dyrk1a-T2WT, Dyrk1a-T2MUT, Dyrk1a-T3WT, Dyrk1a-T3MUT, DYRK1A-T1WT, DYRK1A-T1MUT, DYRK1A-T2WT, DYRK1A -T2MUT, DYRK1A -T3WT, DYRK1A -T3MUT, DYRK1A-T4WT, DYRK1A-T4MUT, DYRK1A-T5WT, DYRK1A -T5MUT, DYRK1A -T6WT ,DYRK1A -T6MUT, DYRK1A -T7WT and DYRK1A -T7MUT, respectively) were synthesized (Sangon Biotech Comp, Shanghai, China) and inserted with the backbone respectively. All the constructions were confirmed by sequencing (Sangon Biotech Comp, Shanghai, China) and then extracted and purified using the EndoFree Mini Plasmid Kit (TIANGEN, Beijing, China) for transfection. Above-described gene sequences were listed in Additional file1: Table S1
Cell transfection and luciferase reporter assays
hnRNPA2B1 siRNA or scrambled siRNA control (Tskingke, Biological Technology, Beijing, China) were transfected with the riboFECT™ CP Transfection Kit (Ribobio, Guangzhou, China) at a final concentration of 100 nM. Expression of related genes was confirmed by qPCR and western bolt. Sequences of siRNA in this study were listed in Additional file1: Table S1
For luciferase reporter assays, 5 X 104/well PC3 or Raw264.7 cells in 24-well plates were co-transfected with 200ng luciferase reporter vectors described above, 20 ng Renilla luciferase vector (pRL-CMV; Promega, Madison, WI, USA), and 80ng miRNA-378a-3p mimic or scrambled control (Genomeditech, Shanghai, China) using Lipofectamine 3000 (Invitrogen, USA) according to the manufacturer’s instructions. Forty-eight hours after transfection, luciferase activities were measured with the Dual-Luciferase Reporter Assay System (Promega, Madison, WI, USA). Reporter luciferase activity was normalized to the internal control Renilla luciferase activity in all samples. Primers for qPCR were listed in Additional file1: Table S1
Lentiviral vector infection
The lentiviral vectors containing miRNA-378a-3p mimic or miRNA-378a-3p inhibitor, shRNA of MAOA or Dyrk1a, and relevant controls were constructed and packaged into lentivirus respectively by Genomeditech Comp (Shanghai, China).
For infection experiment, 1.5×105 PC3 cells, 1×106 bone marrow-derived macrophages (BMMs) or RAW264.7 cells were infected with related lentivirus (MOI = 10 for PC3 and MOI = 100 for BMMs or RAW264.7) along with 10 µg/ml polybrene dissolved the culture medium. Culture supernatant was replaced by fresh medium containing 10% FBS 24h after infection. Expression of related genes and microRNAs were confirmed by qPCR and western bolt. Above-described gene sequences were listed in Additional file1: Table S1
Cell proliferation
Cell proliferation was measured by CCK-8 assay kit (Dojindo, Kumamoto, Japan). PC3 cells were cultured in the 96-well plate at an initial density of 2000 cells/well and were incubated with CCK-8 for 2 hrs at 37°C. The absorbance values of CCK8 staining were measured at 450 nm using a BioTek Synergy HT microplate reader.
Apoptosis and Cell Cycle assay
Apoptosis and cell cycle assay were processed with an Annexin V-Alexa Fluor 647/PI Kit (Yeasen, Shanghai, China) and Cell Cycle Analysis Kit (Yeasen, Shanghai, China), according to the manufacturer’s protocol. Briefly, 106 cells were collected and dual-incubated with Annexin V- Alexa Fluor 647 and PI for flow cytometry assay. For cell cycle analysis, 105 cells per well were seeded in 6-well plate, fixed in 70% ethanol overnight, and stained with PI in staining buffer for 30 min at 37℃. The procedure was protected from light, then collected for flow cytometry assay within 5 hours and analyzed using the flowjo analysis software.
Transwell assay
For transwell assay, 5 × 104 PC3 cells were seeded in the upper chamber (Corning, NY, USA) with 150 µl DMEM Basic Medium, and the lower chamber was loaded with 600 µl DMEM containing 10% FBS. After incubation for 24h, transmigrated cells (on the lower surface of membrane) were fixed with 4% paraformaldehyde for 15 mins, and then stained with 1% crystal violet (Sigma-Aldrich, St. Louis, MO, USA) for 15 mins at room temperature. After that, photograph and cell number count were carried out under a microscope in five random fields.
Induction of osteolysis
BMMs were isolated from the bone marrow of six-week-old male BALB/C mice as previously described [13]. Briefly, Bone marrow cells were collected from tibia and femur to incubate with alpha-MEM supplemented with 10% FBS and 1% penicillin/streptomycin for 48 hours. Non-adherent cells were collected and seeded on 24‐well plates at a density of 5.0 × 105 cells/well and incubated in the presence of M‐CSF (25 ng/mL, PeproTech, Rocky Hill, NJ, USA) for 48 hours to obtain BMMs. BMMs were further stimulated with M‐CSF (25 ng/mL) and RANKL (100 ng/mL, PeproTech) for osteolysis. Culture media were changed every 3 days.
TRAP staining
For TRAP staining, cells were first washed three times with PBS after the culture medium was removed and fixed in 4% paraformaldehyde for 15min, followed by stained using a TRAP staining kit (Nanjing Jiancheng Bioengineering Institute, Nanjing, China) according to the manufacturers’ instructions. After 30 min, staining solution was washed off and the TRAP activity was analyzed by colorimetry. At the same time, the number and size of multinucleated (more than three nuclei) osteoclasts were analyzed and calculated by the imageJ software. TRAP staining for paraffin-embedded tissue sections was carried out by Runnerbio biotech. Comp (Shanghai, China) with similar methods. N.Oc/BS (number of osteoclast per bone surface) and ES/BS (eroded surface per bone surface) were used to measure the number and size of osteoclasts in the mouse bone marrow.
RNA isolation and qRT-PCR analysis
Total RNA was extracted using TRIzol (Thermo Fisher Scientific). The EV-delivered microRNA was extracted using the exoRNeasy Mini Kit (Qiagen, German). MicroRNA reverse transcription and qRT-PCR were carried out using Taqman miRNA reverse transcription kit (Thermo Fisher Scientific) and Taqman premix (Takara, Shiga, Japan) respectively. The specific reverse primers and qRT-PCR Taqman probes for miR-378a-3p and snRNA U6 (internal normalization control) were purchased from Thermo Fisher Scientific. For mRNA expressional analysis, cDNAs were reverse transcribed from 2 µg total RNA with a Prime-Script RT kit (Takara, Shiga, Japan) and amplified with the SYBR-Green Real-time PCR Master Mix (Applied Biosystems, Thermo Fisher Scientific). The mRNA expression level of β-actin was used as an internal normalization control. Comparative quantification was performed by using the 2-ΔΔCt method. All primers are available in the Additional file1: Table S1.
Western blot and co-immunoprecipitation (co-IP)
Nuclear and Cytoplasmic Extraction Reagents (Thermo Fisher Scientific) supplemented with protease inhibitor (Thermo Fisher Scientific) were used to isolate and purify cytoplasmic and nuclear protein in 1×107 cultured cells. RIPA (Millipore) supplemented with protease inhibitor and PMSF (Thermo Fisher Scientific) was used to isolate total protein from either cultured cells or clinical tissue samples.
For western blot, after quantified by the Pierce BCA Protein Assay Kit (Thermo Scientific, Waltham, MA, USA), 40 µg of total proteins were separated by SDS-PAGE and transferred to PVDF membrane (Millipore, Bedford, MA, USA). The membrane was blocked with TBST containing 5% BSA at room temperature for 1h and then incubated with the relevant primary antibodies at 4°C overnight, which was then probed by an HRP-conjugated secondary antibody at room temperature for 1h. The relevant proteins were visualized by the ECL (electro-chemiluminescence) detection instrument (Thermo Fisher Scientific) plus HRP substrates.
For co-IP, whole cell lysates were prepared using a lysis buffer containing 50 mM Tris (pH 7.5), 120 mM NaCl, 0.5% NP-40, 5 mM EDTA and protease and phosphatase inhibitors (Thermo Fisher Scientific). Total protein (100 µg) was incubated with 5µg specific antibodies and 20 µl protein G-sepharose beads (Thermo Fisher Scientific) on shaker at 4°C overnight. After washed by Chilled PBS for 4 times (5mins each), the beads-antibody complex was boiled for 10 min to obtain protein supernatant captured by the protein G-sepharose beads for western blot. β-actin was used as a control for input. Information for all antibodies is available in Additional file1: Table S2.
EVs isolation and characterization
DMEM medium with 10% EV-depleted FBS (Thermo Fisher Scientific) was used for cell culture before isolation EVs from culture medium. After using a gradient centrifugation (300xg for 10 min, 2000xg for 10 min and 10000xg for 40min), the supernatant was filtered using a 0.22µm PVDF filter (Millipore, USA) and followed by the ultracentrifugation at 10,0000g for 90min to harvest EVs deposition. EVs were resuspended in PBS to determine EVs size distribution, concentration and morphology by nanosight tracing assay, western blot assay and transmission electron microscopy (TEM) respectively, which was described in our previous work[10], according to Minimal Information 2018 for Studies of Extracellular Vesicles (MISEV2018) guidelines[14].
EVs labelling and tracking
Purified EVs were labeled with the lipophilic membrane dye PKH67 (Sigma, USA) according to the manufacturer’s instruction. Labeled EVs were washed with PBS and centrifuged again at 10000×g for 70 min at 4°C for incubation with BMMs (5 × 104 cells per well in a 24-well plate at a concentration of 25µg/mL for 24 h).
For EVs education experiments in vivo, 100 µg/kg EVs were inoculated in mice through tail intravenous injection every other day for 3 weeks. For EV-tracking experiments in vivo, 10µg/kg purified and PKH67 labeled EVs were injected 24h before tissue collection.
Chromatin immunoprecipitation (ChIP) assays
The cell extraction was prepared and the experiment was performed according to manufacturers’ instructions by using a ChIP assay kit (Cell Signaling Technology, Danvers, MA, USA). Briefly, ChIP assays were performed using anti-NFATC1 antibody (Santa Cruz Biotechnology, USA) or IgG (Cell Signaling Technology, USA) as a control. After extraction of ChIP DNA, specific fragments (less than 200 bp) containing potential binding sites or control sites were amplified and analyzed by qPCR and sequencing. NFATC1 relative enrichment was calculated by the formula provided in the protocol. Primers used for ChIP assay are available in Additional file1: Table S1.
RNA immunoprecipitation (RIP) assay
RIP assays were performed using a Magna RIP RNA-Binding Protein Immunoprecipitation kit (Millipore, USA). Briefly, cells and EVs were collected and lysed in chilled lysis buffer supplemented with protease inhibitors and RNase inhibitors. Lysates were centrifuged at 14,000×g for 10 min to harvest supernatant for RIP and input (10% volume). The supernatant was incubated with 3 µg anti-hnRNPA2B1 antibody (abcam, England) or IgG (Cell Signaling Technology, USA) in RIP Buffer along with 30 µL A/G protein magnetic beads on rotating overnight at 4°C. Then, the magnetic beads were washed five times, and coimmunoprecipitated miRNAs were extracted using standard RNA isolation method mentioned above. The isolated miRNA was reverse transcribed and then analyzed by qRT-PCR. In addition, miR-378a-3p fold enrichment in immunoprecipitated samples is presented as percent input and compared with IgG isotypic control.
Intratibial injection
Six-week-old male BALB/C athymic nude mice (SLAC, Shanghai, China) were housed and manipulated according to the protocols approved by the Renji Hospital Medical Experimental Animal Care Commission. To establish a bone metastasis model, 2× 105 PC3-con and PC3-378OE cells were injected intratibially into nude mice, respectively, with treatment of GW4869 (2mg/kg, sigma) intraperitoneally injected every 2 days. Five weeks later, mice were sacrificed and tibiae were collected and fixed in 4% formaldehyde for H&E, IHC(Immunohistochemical) staining and high-resolution microCT(Inveon, Siemens, Germany) to evaluate bone destruction. For high-resolution microCT, the average bone volume/total volume (BV/TV) values and bone mineral density (BMD) of the same tibial lesion areas in each group were analyzed.
Immunofluorescent (IF) staining
Cells were seeded on cover slides placed in 24-well plate and cultured in DMEM medium supplemented with 10% FBS and maintained at 5% CO2 at 37°C for 48 h. Adherent cells on cover slides were fixed with 4% paraformaldehyde for 15mins at room temperature. Cells were permeabilized with 0.3% Triton X-100 and then blocked with 10% normal donkey serum (GeneTex, Irvine, California, USA) for 1 hour at room temperature. After incubated with relevant primary antibody (1:200, diluted in PBS with 1% normal donkey serum) at 4°C overnight, cells were first washed with PBS buffer three times (10mins each) and in turn incubated in dark with Alexa Fluor-594 or Alexa Fluor-488 conjugated secondary antibody (Thermo Fisher Scientific) at room temperature for 1 h. Cells were washed with PBS three times again before mounted with DAPI (Thermo Fisher Scientific). Images of IF staining were observed and photographed by a microscope (Leica DFC420C). All antibodies are available in Additional file1: Table S2.
H&E staining and Immunohistochemical (IHC) staining
H&E staining and Immunohistochemical (IHC) staining for paraffin-embedded tissue sections were carried out by Runnerbio biotech. Comp (Shanghai, China). Tissues were fixed in 4% paraformaldehyde overnight and embedded in paraffin. Paraffin-embedded tissue sections were dewaxed in xylene for 5mins and then hydrated in 100, 95, 85 and 70% ethanol successively. After inactivating endogenous peroxidase in disodium-hydrogen phosphate-2-hydrate, these sections were blocked in 10% donkey serum for 1h at room temperature for IHC staining. After serum blocking, sections were incubated with primary antibody (1:200) at 4°C overnight. After washed with PBS for three times (10 min each), sections were incubated with horseradish peroxidase-conjugated secondary antibody (Vector, Burlingame, CA, USA) for 1 h at room temperature. Sections were then washed with PBS again for three times and were visualized with DAB (Sangon Biotech, Shanghai, China) staining and hematoxylin counterstaining (Beyotime, Shanghai, China). Images were acquired under a microscope (Leica DFC420C) in the same exposure conditions. The effectiveness and specificity of primary antibodies were checked before IHC staining by no-primary antibody control assay. All antibodies are available in Additional file1: Table S2.
Clinical samples
The investigation has been conducted in accordance with the ethical standards and according to the Declaration of Helsinki, national and international guidelines as well as the Committee for Ethical Review of Research Involving Human Subjects at Ren Ji Hospital. Human PCa tissue samples for western blot assay and IHC staining, paired adjacent normal tissue samples for western blot assay and non-paired benign mammary hyperplastic samples for IHC staining were obtained from department of urology, Ren Ji Hospital (Shanghai, China). Written informed consents were obtained from all patients for the application of the specimens used in the study. All clinical data of patients participated in the study were summarized in Additional file 1: Table S3.
Statistical analysis
Data were expressed as mean ± SEM from triplicate experiments. Group differences were analyzed using independent Student’s t-test or analysis of variance (ANOVA). Genes differentially expressed between the test and control groups in the GEO datasets (http://www.ncbi.nlm.nih.gov/geo/) were identified using the Limma R package[15]. And we download the TCGA-PRAD datasets from the TCGA RNA-seq database (https://xena.ucsc.edu/public/), the R package “survival” was used to evaluate the association of all candidate genes with overall survival (OS), disease free survival (DFS), disease free interval (DFI), and progress free interval (PFI) [16]. Results were considered as statistically significant when p < 0.05.