Cell culture and Transfection
Breast cancer cell line MCF7 and 293T cells were grown in Dulbecco`s modified Eagle`s medium (DMEM, # 12800-017, Gibco Island, NY, USA) containing 10% fetal bovine serum (FBS, Gibco Island, NY, USA) and 1% penicillin-streptomycin. The cells were grown in a 5% CO2 incubator at 37°C. Full-length human DUBs plasmids were cloned into the pDEST-CMV6 vector with an SRT tag at the N-terminus, and the plasmids are as following: USP3, USP21, USP22, USP25, USP28, USP28, USP35, USP36, USP39, UCH-L1, UCH-L5, and BAP1. To generate a catalytic residue mutation, a site-direct mutagenesis PCR was performed using a site-direct mutagenesis kit (#A14604, Invitrogen) according to the manufacture`s protocol. The plasmid was as followed: USP21 C211A, USP35 C434A, and BAP1C91A. Transfections of DUBs plasmids were performed using transfectamine 2000 reagent (# 11668-019, Invitrogen, Waltham, MA, USA) according to the manufacturer`s protocols.
Western blotting and immunoprecipitation
MCF7 were lysed in lysis buffer (50 mM Tris-HCl, pH 7.5, 1 mM EDTA, 10% glycerol, 300 mM NaCl and 1% Triton-100) and then incubated for 20 min on ice and centrifuged at 13,000 rpm for 20 min at 4°C. Supernatants were collected and the protein was quantified. Western blotting was performed SDS-PAGE gels. Proteins were transferred to polyvinylidene fluoride (PVDF) microporous membranes (# IPVH00010, Millipore, Billerica, MA, USA). Subsequently, the membranes were incubated with TBS-T (20 mM Tris-HCl, pH 7.5, 0.05% Tween 20, and 150 mM NaCl) containing 5% skim milk or 5% bovine serum albumin (BSA) for blocking for 1 h and incubated overnight at 4°C with primary antibodies. Primary antibodies used following: anti-Ub (#SC-166553m Santa Cruz Biotechnology, Santa Cruz, CA, USA), anti-SRT, anti-BAP1 (#SC-28383, Santa Cruz Biotechnology, Santa Cruz, CA, USA), anti-Med1(#SC-8998, Santa Cruz Biotechnology, Santa Cruz, CA, USA), and anti-β-actin (#SC-8432, Santa Cruz Biotechnology, Santa Cruz, CA, USA). Then, the membranes were incubated for 2 h with the secondary antibody. Blots were detected using an ECL reagent solution (# LF-QC0101, Young-In Frontier Seoul, Korea). The immunoprecipitation (IP) experiment performed to investigate protein interaction. Cell lysates were incubated with an antibody (anti-Med1) 4°C overnight and for 2 h with protein A/G PLUS-Agarose beads (# SC-2003, Santa Cruz Biotechnology, Santa Cruz, CA, USA). Samples were collected by centrifuged at 13,000 rpm for 10 min at 4°C and washed three times for 5 min each with TBS-T. The samples were boiled in 4X SDS sample buffer for 10 min and analyzed using western blotting.
Luciferase reporter assay
MCF7 cells were transfected with the ERE-Luc reporter luciferase plasmid cloned with pRL-TK-Luc vector and the indicated plasmids (pDEST-CMV6-DUBs). To normalize luciferase activity, Renilla luciferase reporter control vector was co-transfected. At 48 h after transfection, the cells were collected and performed the dual-luciferase reporter assays. Luciferase activity was measured following the manufacture’s protocol (Promega, Madison WI, USA). The firefly luciferase activity was divided by Renilla luciferase activity to figure out the relative luciferase activity. The data represent the average values from three independent experiments.
Quantitative RT-PCR (qPCR)
Total RNA extraction performed according to the manufacture`s protocol of the TRIzol reagent (#10296010, Ambion, ThermoFisher, USA). And cDNA was synthesized using Moloney murine leukemia virus reverse transcriptase (MMLV-RT) and oligo-dT primers (Promega, Madison, WI, USA). qPCR was performed in triplicate using the SYBR Green PCR Master Mix (Takara Bio Inc., Bio Inc. Shiga, Japan) and ABI Prism 7500 Real-Time PCR system (Applied Biosystems). The β-actin transcript was used as an internal control for all samples, and the gene-specific mRNA level was normalized to the level of β-actin mRNA. The expression of each mRNA was determined using the 2-ΔΔCT -threshold cycle method. The following primers were used: Med1: forward 5`-AGTATCATGGGCTCAGCTCC-3’ and reverse 5`-GGTGAGCCCATCATCGACAATTC-3’. BAP1: forward 5`-CCACAAGTCTCAAGAGTCACAG-3` and reverse 5`-CTGCACCATCTGTGTGGTT-3’. uPAR: forward 5`-CGGGCTCCAATGGTTGCCA-3` and reverse 5`-CAGAGTGAGCGTTCGTGAGTG-3’. β-actin: forward 5`-GCTCCTCCTGAGCGCAAG-3` and reverse, 5`-CATCTGCTGGAAGGTGGACA-3`.
In vitro migration and invasion assays
The cell migration assay was performed using multi-chamber well, which was separated from the complete culture medium in the bottom chamber by a polyethylene terephthalate membrane filter (8 µm pore size) (Neuro Probe, Inc., Gaithersburg, MD). The 1 x 105 resuspended cells in serum-free medium were transferred into the upper chamber and complete culture medium was incubated in bottom chamber. FBS was used as a chemoattractant. During incubation for 18 h, cells migrated through pores. Non-migrated cells were carefully removed using a cotton swab, and cells migrated undersurface the membrane filter were fixed with cold methanol for 20 min at room temperature and add the crystal violet to the well for staining the migrated cell. The cells on membrane read density of the stained cells at 595 nm using a microplate reader.
The cell invasion assay was performed using Boyden chambers with Matrigel-pre-coated filter inserts (8 µm pore size) (Costar, Corning, NY). A suspension of 1 x 105 cells in the medium was added to the upper chamber while the lower chamber was fill with medium containing 10% FBS. After 18 h of incubation, the cells that had invaded the membrane were fixed and stained with hematoxylin and eosin (H&E). Stained cells in three randomly chosen fields (100X magnification) were photographed and counted. Data represent the average of three individual experiments, and error bars represent the standard error of the mean (SEM).
Cell proliferation assay
The 1 x 104 cells were seeded each well in 6-well plates and allowed to proliferate for 6 days. The medium was changed every 2 days. After six days, the cells were collected, stained with trypan blue, and counted to measure proliferation. The experiments were repeated three times and performed in triplicates.
The MCF7 cells were seed and treated each 10 ng of EGF (#PHG0311, Invitrogen), E2 (#E4389, Sigma-Aldrich), and TGF-β for 24 h and then harvested. The total cell lysates were immunoblotted with anti-Med1 and anti-BAP1.
Statistical analysis
Densitometric analysis was performed using Image J. The paired t-test and two-way ANOVA were performed by GraphPad Prism version 5 (GraphPad Software, La Jolla, CA USA), p-values of *p < 0.05, **p < 0.01, ***p < 0.001 were deemed significant. All results shown are representative data of at least three independent experiments and are presented as the mean ± standard error of the mean (SEM).