Cell culture
All cell lines were originally purchased from the American Type Culture Collection (ATCC) and none of these cell lines were found to be contaminated with mycoplasma during our study. 293T cells were grown in DMEM (Invitrogen, catalog no. 10569010); RWPE-1 cells were cultured with keratinocyte serum-free medium (Invitrogen, catalog no. 10724011) with bovine pituitary extract and human recombinant EGF; LNCaP and DU145 cells were grown in RPMI1640 (Merck, catalog no. R8758); PC3 cells were cultured in F-12 Kaighn’s Modification (HyClone, catalog no. SH30526.01). All media were supplemented with 10% fetal bovine serum (Gibco, catalog no. 10099-141C) and with antibiotics (Thermo Fisher Scientific, catalog no. 15140122).
Immunoprecipitation
Immunoprecipitation was performed as described previously [28]. Briefly, for transfection-based co-immunoprecipitation assays, 293T cells were transfected with the indicated plasmids using Lipofectamine 2000 (Invitrogen, catalog no. 11668019) lysed and immunoprecipitated with anti-FLAG antibody (Sigma-Aldrich, catalog no. F3165) or anti-MYC antibody (Thermo Fisher Scientific, catalog no. MA1-980) combined agarose beads, Cells lysed and immunoprecipitated with anti-Smad4 antibody (Abclonal, catalog no. A19116) combined agarose beads for 12 h at 4°C. The beads were washed three times with the lysis buffer and eluted in SDS sample loading buffer. The eluted proteins were separated by SDS-PAGE, transferred to PVDF membranes (Millipore, catalog no. ISEQ00010) and detected in western blots with appropriate primary antibodies coupled with HRP-conjugated secondary antibody by chemiluminescence (Pierce, catalog no. 32106). For detection of the interaction of endogenous proteins, whole cell extracts were immunoprecipitated with specific antibodies overnight at 4°C. Normal IgG was used as a negative control. After extensive washes, the immunoprecipitates were resolved with SDS sample loading buffer for Western blot analysis.
Ubiquitination of Smad4.
HEK293T cells were transfected with the indicated constructs. 36 h after transfection, cells were harvested and lysed in lysis buffer. Anti-HA (ABclonal: AE008) antibody was used to detect polyubiquitinated Smad4. For detecting the endogenous ubiquitination of Smad4, PLK1 overexpression in PC3 cells were lysed in lysis buffer. Then, the ubiquitination of Smad4 was analyzed by immunoprecipitated with anti-Smad4 (ABclonal: A19116) antibody and immunoblotted with anti-Ub (ABclonal: A19686) antibody or anti-Smad4 antibody.
Cycloheximide (CHX) chase assay.
Cells were incubated in 50 μg/ml cycloheximide (Cell Signaling Technology, catalog no. 2112) for indicated times. Then, cells were harvested and lysed in 2 × Loading sample buffer. Protein level was determined by western blot analysis.
Western blot
Cells pellets were harvested and resuspended in lysis buffer (600mM NaCl, 1% Triton X-100 in PBS, 1 x protease inhibitor). Protein concentration was measured using the BCA protein assay kit (Thermo Fisher Scientific, catalog no. 23227). Western blot analysis was performed in accordance with standard procedures. Anti-PELO antibody (ab140615) was purchased from Abcam; anti-PELO (SAB1401719) and anti-FLAG (F3165) antibodies were purchased from Merck; anti-Smad4 (A19116), anti-HA (AE008), anti-Ubiquitin (A19686), anti-GAPDH (AC002) and anti-MYC tag (AE010) antibodies were purchased from ABclonal; anti-PLK1 antibody (4513S) was purchased from Cell Signaling Technology; anti-MYC (MA1-980), anti-V5 (MA5-15253), anti-ITGA1 (PA5-79525) and HRP-conjugated secondary antibodies were purchased from Thermo Fisher. Signals were visualized with the Super Signal West Pico PLUS Chemiluminescent Substrate kit (Pierce, catalog no. 34577).
Immunohistochemistry (IHC) assays
To explore the expression of PELO in PCa tissues and adjacent tissues, two PCa tissue chips (Catalog No. HProA 150CS01, HProA150PG02) were purchased from Outdo Biotech (Shanghai, China). We first deparaffinized and rehydrated the tissue chips, retrieval antigen 5 min at 121°C, blocked endogenous enzyme activity 30 min at room temperature using 3% H2O2-methanol, blocked the chips 1 h with 5% BSA. We incubated the chips with the PELO primary antibody (Abcam, catalog no. ab140615) (diluted at 1:50) overnight at 4 °C. Then we incubated the tissue chips with EnVision-HRP secondary antibody for 1 h, the signals were detected by diaminobenzidine followed by hematoxylin counterstaining. Aperio ScanScope slide scanner was used for viewing the signals. Of note, the result was assessed according to the intensity of staining (0, 1+, 2+, and 3+) and the percentage of positive cells (0 (0%), 1 (1–25%), 2 (26–50%), 3 (51–75%), and 4 (76–100%)) by two experienced pathologists. Finally, the final staining score was calculated and analyzed.
Xenograft tumor model and in vivo metastasis analysis
30 male athymic nude mice at 4 weeks of age were used according to the protocols approved by the ethical committee of Shaanxi Normal University. Briefly, for in vivo metastasis analysis, male nude mice (5 per group) were injected i.v. via the tail vein with 1 × 106 PC3 sublines (control shRNA, shPELO-1 and shPELO-2). Six weeks later, nude mice were sacrificed, and the lung and liver metastases were examined by H&E staining. For the peptide experiment, 15 male nude mice were injected with 1 × 106 PC3 cells through tail vein, after 2 days, 7 nude mice were injected with PBS through tail vein every 2 days, the others were treated with peptide every 2 days. 50 days later, the liver and lung were dissected from each of the mice, then H&E staining was used to exam the metastases status.
RNA isolation and real-time PCR
Total RNA was extracted using RNeasy Mini kit (Tiangen, catalog no. DP430) according to the manufacturer’s instructions. First strand cDNA was synthesized using 1 ug of total RNA and Superscript II (Thermo Fisher Scientific, catalog no. 4368814). Real-time quantitative PCR was performed in triplicates with SYBR Green qPCR mix (Thermo Fisher Scientific, catalog no. 4472908). The relative amount of specific mRNA was normalized to GAPDH.
Cell viability and proliferation assays.
Cells treated with PELO shRNA or control shRNA lentivirus (1×103 per well) were seeded in 96-well plates. Cell viability and proliferation were determined with XTT assays (Roche, catalog no. 11465015001) at designed time points by measuring the absorbance at 450 nm, following the manufacturer’s instructions. Values were obtained from three replicate wells for each treatment and time point. The results are representative of three independent experiments. Significance was calculated by a two-tailed t test.
Transwell invasion and migration assay
Standard 24-well Boyden invasion chambers (BD Biosciences) were used to assess cell invasiveness following the manufacturer’s suggestions. Briefly, cells were trypsinized, rinsed twice with PBS, resuspended in serum-free medium at 2.5 × 105 cells/ml. 200 µl of cell suspension was transferred into 8-μm Transwell inserts (Corning Costar, catalog no. 3422) with (invasion) or without (migration) 100 µl Matrigel (diluted with serum free medium to 250µg/ml) coating (BD Biosciences, catalog no.356230). 10% serum-containing medium was added in the lower chambers. Following 48 h incubation, chambers were fixed in 3.7 % formaldehyde, after permeabilized with methanol, stained with Wright-Giemsa (Sigma-Aldrich, catalog no. WG16) for manual counting. A two-tailed t-test was employed to perform statistical analysis from three replicate inserts.
Chromatin immunoprecipitation (ChIP).
The ChIP experiment was performed as previously described [29]. Briefly, PC3 cells were crosslinked with 1 % formaldehyde (Merck, catalog no. F8775) and stopped the reaction with 125 mM glycine (Merck, catalog no. G8898). The nuclei were isolated from cells and then suspended in SDS lysis buffer. Nuclear extracts were sonicated to generate an average size of 400bp chromatin fragment. In each reaction, 6 µg of anti-Smad4 antibody (ABclonal, catalog no. A19116), anti-TEAD1 antibody (ABclonal, catalog no. A6768) or normal rabbit IgG (CST, catalog no. #2729) were incubated with 70 µl of Dynabead protein G (Invitrogen, catalog no. 10004D) slurry in IP buffer for 12 h. Then the fragmented chromatin was incubated with bead/antibody complexes overnight. After washing and reverse-crosslinking, the precipitated DNA was purified with MinElute PCR Purification Kit (Qiagen, catalog no. 28006) and the target DNA fragments were analyzed by qPCR. Enrichment was calculated relative to input.
Lentiviral constructs, lentivirus production and infection.
The shRNA constructs targeting PELO were ordered from Merck. In detail, 293T cells were trypsinized and seeded into 3.5-cm plates with normal DMEM medium containing 10 % FBS, 1 % penicillin and streptomycin. The normal DMEM medium was replaced with 2 ml low glucose DMEM (Invitrogen, catalog no. 21885025) before transfection. For second generation lentiviral production, 1.5 μg shRNA construct, 0.375 μg pMD2.G (envelope plasmid), and 1.125 μg psPAX2 (packaging plasmid) were diluted to 100 ul using Opti-MEM (Invitrogen, catalog no. 11058-021) and combined with 100 ul Opti-MEM containing 8 µl Lipofectamine 2000 (Invitrogen, catalog no. 11668019). This mixture was incubated at room temperature for 20 min and added to the 2 ml medium covering the 293T cells. The medium was changed to fresh medium after 24 h and the virus-containing medium was harvested every 24 h up to three times. Lentivirus was passed through 0.45 μm filter unit and stored at −80 °C. For viral transduction, Viral supernatants containing 8 μg/ml polybrene (Merck, catalog no. H9268) were added to PCa cells that were seeded 24 h before infection at 70–80% confluence. For lentivirus-mediated knockdown experiment, virus was removed and replaced by normal medium with antibiotics after 24 h, after which cells were selected with 1 μg/ml puromycin (Merck, catalog no. P9620). When uninfected control cells were completely killed, the target cells were cultured in normal growth medium with 0.5 μg/ml puromycin for further experiments.
GST Pull-down Assay
PELO full length was cloned in frame with the glutathione S-transferase (GST) gene of pGEX-6P-1 and the resulting GST fusion proteins were expressed in Escherichia coli BL21, induced by 0.1 mM isopropyl-b-D-thiogalactopyranoside (IPTG) and solubilized from bacteria in lysis buffer (1% Triton X-100 in PBS) by sonication. After centrifugation for 10 minutes at 4°C, the supernatant was incubated with the glutathione-Sepharose 4B beads (Thermo Fisher Scientific, catalog no. 16100) at 4°C overnight. Beads were harvested through centrifugation and washed three times in cold PBS to remove nonspecific binding. GST and GST-fusion proteins were bound to glutathione-Sepharose beads followed by SDS-PAGE. The PC3 cell lysates were treated with DNase I (Thermo Fisher Scientific, catalog no. 18047019) for 30 minutes at 37°C to remove the genomic DNA contamination before mixed with GST fusion protein which adsorbed to Sepharose beads. The binding reaction was carried out overnight at 4°C in 1 mL binding buffer (20 mmol/L Tris-HCl at pH 8.0, 150 mmol/L NaCl, 1 mmol/L EDTA, 10% glycerol and 0.1% NP-40). After extensive washing, specifically bound proteins were subjected to 10% SDS-PAGE followed by western blot analysis.
Soft agar assays
About 400 PC3-control, PC3-shPELO-1 and PC3-shPELO-2 cells were suspended in 0.2 ml of prewarmed 0.35% SeaPlaque agarose/MEM/5% fetal bovine serum and pipetted on top of 0.3 ml of 0.7% SeaPlaque agarose/MEM/5% fetal bovine serum gelled onto a well of a 24-well plate, then 0.4ml medium was added on top of the cells. Cells were incubated for 15 days, at 37 °C and 5% CO2, and fresh medium was changed every three days. The colony spots were counted through eye vision.
Statistical analysis
All statistical analyses were performed using GraphPad Prism version 5.0 software (GraphPad, San Diego, CA, USA). Data were obtained from the cBioPortal for Cancer Genomics [30, 31], and GEO database [32, 33]. Statistical tests for patients with gene expression were calculated using Mann-Whitney U test. Kaplan Meier survival analysis was used to assess the impact of gene expression levels on prostate cancer prognosis and survival. P value < 0.05 was considered to be statistically significant, all error bars in graphical data represent mean ± SD.