Tissues and Cell Lines
The present study was approved by the local Ethics Committee. Written, informed consent was obtained from all patients, who were verified as negative for human immunodeficiency virus (HIV) and hepatitis virus C (HCV). We gathered liver tissue samples from nine HBV-related HCC patients undergoing hepatectomy at The Second Affiliated Hospital of Chongqing Medical University. HCC was confirmed by pathologic or radiographic examinations. Normal liver cell line HL7702 and HCC cell lines Bel7402, SMMC7721, MHCC97H, and MHCCLM3 were purchased from Cell Bank of Type Culture Collection of Chinese Academy of Sciences, Shanghai Institute of Cell Biology, Chinese Academy of Sciences. HepG2 cell and Huh7 cell were purchased from ATCC (Rockville, MD). All cells were cultured in high-glucose DMEM (HyClone, Waltham, MA) supplemented with 10% fetal bovine serum (Gibco, San Diego, CA) and 100 IU/mL of penicillin, 100 µg/mL of streptomycin, maintained at 37°C with 5.0% CO2.
Reagents and antibodies
Eight-plex iTRAQ reagent kits were acquired from Applied Biosystems (Foster City, CA, USA). Monoclonal antibodies against human CRP were obtained from HyTest (Finland, Turku). Monoclonal antibodies against UGDH, EphB3, ENO2, ANXA2, KRT5, MSH2, SHC1, HSP90B1, MAPK, p-MAPK, ERK, p-ERK and HIF1α were purchased from Abcam (Cambridge, USA). CRP specific Stealth Select RNAi™ siRNA (NM_000567), Stealth RNAi™ Negative Control siRNA and Lipofectamine Max transfection reagent were obtained from Santa Cruz (California, USA). Small interfering RNA against human EphB3 (ID 146498, ID 146499) were purchased from Invitrogen (Grand Island, NY). IP lysis buffer was purchased from Beyotime (Shanghai, China). Protein A/G agarose beads from GE Healthcare (Little Chalfont, UK). CytoSelect™ 24-Well Cell Migration and Invasion Assay kits (8 µm, colorimetric format) were purchased from Cell Biolabs (San Diego, CA, USA).
RT-PCR analysis
RT-PCR analysis was performed as described previously [21]. Total RNA extraction was performed according to the manufacturer’s instructions. The cDNA was produced by reverse-transcription of the total RNA by employing the Promega Reverse Transcription System A3500. An ABI 7900HT System (Applied Biosystems, Foster City, CA) was used for RT-PCR using gene-specific primers for CRP (Hs00437486_CE), EphB3 (Hs00244637_CE), GADPH (Hs02758991_g1). Fold enrichment of indicated gene expression was calculated using ΔΔCT method or 2−ΔΔCT [21]. The experiments were performed in triplicate.
Western blot analysis
Western blot analysis was performed as previously reported [22]. Tissues/cells were lysed with IP lysis buffer, and a BCA Protein Assay Reagent Kit was used to determine the protein concentration. Protein samples were separated by SDS-PAGE and then electro-blotted onto PVDF membranes. Membranes were blocked with BSA in Tris-buffered saline solution with Tween-20 (TBS-T) for 2 h at room temperature. Subsequently, the membranes were incubated with the primary antibodies (1:1000-1:2,000 dilution), overnight at 4˚C and then with HRP-conjugated secondary antibodies at a dilution of 1:5,000 after three wahses with TBST buffer. Finally, membranes were visualized with an ECL detection instrument (Bio-Rad Laboratories, Hercules, CA, USA).
Immunohistochemistry
Immunohistochemistry analysis was performed as previously reported [23]. Briefly, HCC tissues were dehydrated in graded alcohol and embedded in paraffin wax. A thickness of 6 mm prepared on a glass slide was performed in xylene and rehydrated by ethanol and placed in PBS. Antigen retrieval was performed by heating in a microwave oven for 15 minutes with citric acid buffer (0.1 M, pH.6). After dewaxing the sections, endogenous peroxidase activity was blocked by 3% H2O2 in PBS. Non-specific adsorption was minimized by pre-incubating a portion of 10% normal donkey serum for 60 minutes, and CRP and EphB3 were detected using specific antibodies. Images were taken with a Nikon microscope (Nikon, Melville, NY, U.S.A.).
RNA Interference
Cells were trypsinized, then plated on a 6-well plate at an appropriate concentration per well with specific siRNAs or negative control siRNA using the Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA). Three days after the transfection, cells were harvested to examine the protein expression or used for experiments.
Migration, Invasion and wound healing assay
SMMC7721 cells and Huh7 cells were pretreated with 100 nm of CRP-siRNA as described above, then subjected to migration, invasion and wound healing assay. Cells’ viability was determined by trypan blue dye exclusion to be over 95%.The migration and invasion assay were performed by using a Transwell Kit according to the manufacturer’s instructions. For wound healing assays, cells were approximately 100% confluent in 6-well plate, then 200-µl pipet tip was used to scratch the cell monolayer. The resultant gap was monitored for up to 24 h via a microscope.
Co-Immunoprecipitation (Co-IP) and iTRAQ labeling
After SMMC7721 cells were pretreated with CRP-siRNA or a negative siRNA, cell Lysates were collected and the protein concentration was detected by BCA kit. Then the protein samples were mixed with goat antibodies against CRP, rotating vertically overnight at 4°C. Protein G beads were added to the immune complexes and incubated for 2 h under gentle rotation. The beads were pelleted and washed three times with lysis buffer. Bound protein-complexes were eluted using SDS sample buffer. The eluted protein (300 µg) was precipitated from each pooled group, dissolved, denatured, cysteine blocked, digested and labeled using iTRAQ reagents [Control siRNA, 118 and 121 tag; CRP siRNA 113 and 119 tag] (Supplementary Fig. S1).
Mass spectrometry and Bioinformatic analysis
Labeled peptides were fractionated and purified by immobilized-pH-gradient isoelectric focusing (IPG-IEF), as previously described [24]. Purified peptide fractions were reconstituted in solvent A. The peptides were electrosprayed using a nanoelectrospray ionization source at an ion spray voltage of 2300 eV and analyzed by a NanoLC-ESI-Triple TOF 5600 system (AB Sciex). The mass spectrometer was set in the positive ion mode at a mass range of 300-1800 m/z. The two most intensely charged peptides above 20 counts were selected for MS/MS at a dynamic exclusion of 30 sec [24]. Data were processed by ProteinPilot v2.0 (AB Sciex) and the candidate proteins were identified. Protein identification was based on a threshold of protein score >1.3, a confidence limit of 95%, a false discovery rate of 5%, and an additional iTRAQ ratios >1.3. For quantitation, at least two unique peptides with 95% confidence and a P-value <0.05 were required. The bioinformatic analysis of gene ontology (GO) was performed by the Database for Annotation, Visualization, and Integrated Discovery (DAVID).
Validation of CRP interacting proteins
Co-IP and western blot analyses were performed to validate the proteomic data on some randomly chosen CRP interacting proteins. SMMC7721 cells and Huh7 cells protein samples were collected in lysis buffer. Then CO-IP assay was performed as described above. The protein of UGDH, EphB3, ENO2, ANXA2, KRT5, MSH2, SHC1 and HSP90B1 which may interact with CRP was detected using immunoblotting.
Immunofluorescence assay
Liver cancer cells with a concentration of 1 × 105 cells per dish were cultured in confocal dishes with DMEM supplemented with 10% FBS for 24h. Then cells were fixed with 10% (vol/vol) paraformaldehyde, perforated with 0.1% (vol/vol) Triton X-100 and blocked with 10% (vol/vol) normal goat serum in PBS-T. Cells were incubated for 18 hours in anti-EphB3, anti-MAPK and anti-ERK primary antibodies and subsequently incubated in the appropriate species-specific Alexa fluorescent dye conjugated secondary antibodies (Invitrogen) for 90 min at 37°C. The immunostained cells were viewed by confocal microscopy (Nikon, Melville, NY, U.S.A.).
Human recombinant protein, block antibody, Inhibitor and small interfering RNA treatment
After reaching 70-80 % confluence, HCC cells were seeded in six-well plates (2 ×105cells/well). The cells were treated with the following reagents for different times as needed for the experiment: (a) PBS solution as a control; (b) human recombinant CRP protein (rCRP, ab111647) or CRP antibody or ERK inhibitor (PD098059, 10 µM) alone; (c) rCRP plus ERK inhibitor or EphB3 siRNA or HIF1α siRNA. Doses of the human recombinant protein, block antibody, inhibitor were determined according to previous laboratory characterization and published data. Cell extractions were collected in appropriate time after treatment.