Cell culture
Primary chicken embryo fibroblast (CEF) cells and the continuous CEF cell line DF-1 (CRL-12203; American Type Culture Collection, Manassas, VA, USA) were grown in Dulbecco’s modified Eagle’s medium (DMEM; HyClone, Logan, UT, USA) supplemented with 10% fetal bovine serum (FBS; HyClone, Logan, UT, USA), 1% penicillin-streptomycinsolution (HyClone, Logan, UT, USA) and 2% chicken serum (Sigma, St. Louis, MO, USA). Cells were passaged, cultured and maintained at 37°C in a humidified 5% carbon dioxide incubator. Because CEF cells are difficult to prepare and use for siRNA and overexpression experiments, we used the continuous chicken embryo fibroblast cell line DF-1 (CRL-12203; American Type Culture Collection, Manassas, VA).
Proteome analysis
The sample lysis solution consisted of 7 M urea and 2 M thiourea containing 4% (w/v) CHAPS, 1% (w/v) DTT, 2% (v/v) pharmalyte and 1 mM benzamidine. The proteins were extracted for 1 hr at room temperature with vortexing. After centrifugation at 15,000 rpm for 1 hr at 15°C, the insoluble fraction was discarded and the soluble fraction was subjected for 2D gel electrophoresis. The protein concent ration was measured using the Bradford method (
Bradford, 1976).
IPG dry strips (4-10 NL IPG, 24 cm, Genomine, Korea) were equilibrated for 12-16 hr with a 7 M urea plus 2 M thiourea solution containing 2% CHAPS, 1% DTT and 1% pharmalyte and each strip was loaded with 200 µg of the protein sample. Isoelectric focusing (IEF) was performed at 20°C using a Multiphor™ II electrophoresis unit and an EPS 3500 XL power supply (Amersham Biosciences, UK) according to the manufacturer’s instructions. For IEF, the voltage was linearly increased from 150 to 3,500 V over 3 hr to allow for sample entry and subsequently maintained at a constant voltage of 3,500 V, with the focusing complete after 96 kVh. Prior to the second dimension of the 2D electrophoresis, the strips were incubated for 10 min in equilibration buffer (50 mM Tris-Cl pH 6.8 containing 6 M urea, 2% SDS and 30% glycerol), first with 1% DTT and then with 2.5% iodoacetamide. The equilibrated strips were inserted into the SDS-PAGE gels (20 x 24 cm, 10-16%) and SDS-PAGE was performed using a Hoefer DALT 2D system (Amersham Biosciences, UK) per the manufacturer’s instructions. The 2D gels were run at 20°C for 1,700 Vh and silver stained as described previously (
Oakley et al., 1980), omitting the glutaraldehyde fixation and sensitization steps. The digitized images were quantitatively analyzed using PDQuest (version 7.0, Bio-Rad) per the manufacturer’s protocols. Each spot was normalized using the total intensity of the valid spots. We selected the protein spots that deviated more than two-fold from the control or normal samples as showing significant expression levels.
Functional interactome analysis
Experimental data were integrated and analyzed using GeneMANIA (Montojo
et al., 2014) Cytoscape plugin. CluGO functional analysis was performed using GO: Biological Process with the default CluGO setting. For the list of genes that were associated with “translation,” GO: Biological Process was applied to reconstruct the functional interaction network using the GeneMANIA plugin. The scores and parameters were selected by default. The organic or circular algorithm that determined the node positions based on their connectivity was used to design the network.
siRNA treatment
A total of 1X10
6 fibroblasts were seeded onto 6-well plates and transfected using RNAiMAX (Invitrogen, Carlsbad, CA, USA) as described by the manufacturer. Briefly, 7.5 µL of the RNAiMAX reagent was suspended in 100 µL of Opti-MEM (Gibco-BRL/Invitrogen, Carlsbad, CA, USA) and incubated for 5 min at room temperature. The mixture was added to a 100-µL Opti-MEM solution containing 75 nM siRNAs. Then, the RNAiMAX mixture and probes were added dropwise to the fibroblasts in the culture medium lacking antibiotics. The sequence of siRNA for chicken GRP78 was 5’-CACUUCAUCAAACUCUACA-3’.
Immunoblotting
The primary antibodies for western blotting used in this study are GRP78 (PA5-22967, Thermo Scientific/ Pierce, Rockford, IL, USA), Cell Signaling Technology, MA, USA), p-AKT1 (9275, Cell Signaling Technology, MA, USA), p-AKT (PAB10323, (Abnova, San Francisco, CA, USA) and β-actin (MA1-91399, Thermo Scientific/Pierce, Rockford, IL, USA). Protein extracts (20 µg) were electrophoresed using a NuPAGE 10% Bis-Tris gel system (Invitrogen, Carlsbad, CA, USA) and transferred to nitrocellulose membranes. The membranes were blocked with 5% skim milk in TBST (0.01 M Tris, 0.15 M NaCl and 0.5% (w/v) Tween 20) for 1 hr. The Indicated primary antibodies were incubated at 4°C overnight followed by secondary antibodies were for 2 hr at room temperature. The membranes were washed and incubated with HRP-conjugated secondary antibodies for 1 hr. The ECL (Pierce, Rockford, IL, USA) chromogenic substrate was used to visualize the bands and images were captured on X-ray films. The band densities of scanned X-ray film were analyzed using image J software.
Statistical analysis
All analysis was conducted using the Graph Pad Prism statistical software (Graph Pad Software). An unpaired t test was used for comparisons of the treatment groups and a P-value less than 0.05 was considered statistically significant. The data are presented as the means ± standard errors (SEs) or standard deviations (SDs)