Cell culture and animal immunization
The human PAAD cell lines AsPc-1, BxPc-3, Panc-1, and Mia PaCa-2 were purchased from the American Type Culture Collection (ATCC) (Manassas, VA, USA). All cell lines were cultured according to ATCC standard protocols and incubated at 37°C in a humidified atmosphere of 5% CO2.
Female white leghorn (Gallus domesticus) chickens and nonobese diabetic mice with severe combined immunodeficiency (NOD/SCID) were purchased from the National Laboratory Animal Center, Taiwan, and were maintained in the animal facility of Taipei Medical University.
Bioinformatics analysis
To investigate the association between EphA2 gene expression and PAAD occurrence, we used the Gene Expression Profiling Interactive Analysis (GEPIA; http://gepia.cancer-pku.cn) database to analyze the difference in EphA2 expression in clinical cancer samples and normal samples and to analyze the correlation between EphA2 expression and the PAAD survival rate [23].
Antibody library construction and biopanning
On the basis of the complex protein structure of ephrinA1–EphA2 (Protein Data Bank [PDB] ID: 3CZU), we designed a peptide immunogen for the EphA2 target molecule; the peptide immunogen (EphA2pep) contains Epitope 1, GWDLMQNIMNDMPIYMYSV, and Epitope 2, VSSDFEARHV, which were linked together by using a linker GGGGGGS. EphA2pep contains six consecutive repetitive sequences. After gene synthesis (GENEWIZ), it was constructed on a pET21a vector (Novagen) and transformed to the Escherichia coli BL-21 (DE3) strain for its expression as a recombinant protein. After purification by using Ni2+-charged sepharose (GE Healthcare Life Sciences), the recombinant EphA2pep protein was used for animal immunization. Female white leghorn chickens were immunized through intramuscular injection of 50 μg of recombinant EphA2pep protein mixed with an adjuvant each time. During the immunization, we used Freund’s complete adjuvant (Sigma-Aldrich) the first time and Freund’s incomplete adjuvant (Sigma-Aldrich) all other times. The immunization schedule comprised four immunizations performed at intervals of 7 days. The spleens of the chickens were harvested 7 days after the final immunization to construct an scFv antibody library. The library was constructed in accordance with published protocols, with minor modifications [2].
For panning, the recombinant EphA2 protein was precoated onto the well of a microtiter plate at 4oC overnight. On the next day, the EphA2 protein was removed, and the well was blocked with 3% BSA at room temperature for 1 h. Then, the recombinant library phage solution (1011 phage particles) was added to the well and incubated at room temperature for 2 h. Unbound phages in the supernatants were removed, and the well was washed through pipetting with phosphate-buffered saline with 0.05% Tween 20 (PBST) 10 times. Subsequently, bound phages were eluted with 0.1 M HCl–glycine (pH 2.2)/0.1% BSA elution buffer and neutralized with 2 M Tris base buffer. The eluted phages were immediately used to infect the E. coli ER2738 strain for recombinant phage amplification. Amplified phages were precipitated and recovered through a previously method [4] and were used in the next round of panning. The panning procedure was repeated four times to efficiently enrich anti-EphA2 binding phages. After panning, the total library DNA was purified and transformed into the E. coli strain TOP 10F’ (Invitrogen, a nonsuppressor strain) for scFv expression. The expressed scFv was further purified with Ni2+-charged sepharose in accordance with the manufacturer’s instructions (GE Healthcare Life Science).
Sequence analysis
To sequence the scFv clones of interest, we used the ompseq primer (5’-AAGACAGCTATCGCGATTGCAGTG-3’) complementary to the outer membrane protein A (ompA) signal sequence upstream of the light chain variable region. Next, the website International ImMunoGeneTics information system/V-QUEry and Standardization (http://imgt.org) were used to compile and analyze the sequence data on the basis of the germline genes.
Enzyme-linked immunosorbent assay
The recombinant EphA2 protein (0.5 μg/well) was coated onto the wells of the microtiter plate at 4°C overnight. The wells were blocked with 5% skim milk, and scFv or phage was then added to the wells at room temperature for 1 h. After the wells were washed with PBST, the bound scFv or phage was then detected and developed using horseradish peroxidase (HRP)-conjugated goat anti-chicken light chain antibodies (Bethyl Laboratories) or HRP-conjugated anti-M13 antibodies (GE Healthcare Life Science). Finally, the substrate 3,5,5-tetramethubezidine dihydrochloride (TMB) was added for signal development. The reaction was stopped by adding 1 N HCl, and absorbance was measured by determining optical density (OD) at 450 nm.
Western blotting and immunoprecipitation assay
The recombinant EphA2 protein was transferred onto nitrocellulose membranes (GE Healthcare Life Sciences) after electrophoresis using sodium dodecyl sulfate–polyacrylamide gel (SDS-PAGE) or native-polyacrylamide gel (Native-PAGE), and the membranes were incubated with using purified scFv antibodies to determine binding reactivity. The membranes were blocked with 5% skim milk and then incubated with scFv at room temperature for 1 h. After washing with PBST, the membranes were detected and developed using HRP-conjugated goat anti-chicken light chain antibodies. Finally, the 3,3’-diaminobenzidine substrate was added for color development until the desired color intensity was reached.
For the immunoprecipitation assay, 300 μg of each PAAD cell lysate was incubated with 50 μg of anti-EphA2 scFv (scFv was fused with a His tag) at 4°C overnight. On the next day, 30 μL of Ni2+-charged sepharose was added to the mixture and incubated for 1 h at 4°C. After three rounds of washing with Ni-NTA wash buffer (50 mM NaH2PO4, 300 mM NaCl, and 10 mM imidazole, pH 8.0), the scFv-bound sepharose beads were resuspended in 50 μL of PBS buffer. Subsequently, the sepharose solution was denatured at 95°C for 10 min and analyzed using SDS-PAGE. After the proteins were transferred to a polyvinylidene fluoride membrane, the membrane was detected using the anti-EphA2 antibody (R&D Systems) and anti-His (Proteintech Group) antibody at 4°C overnight. On the next day, after washing with PBST, the membrane was incubated with HRP-conjugated secondary antibody (Jackson ImmunoResearch Laboratories). Finally, the chemiluminescence substrate was added for luminal signal detection.
Flow cytometry analysis
Four PAAD cells AsPc-1, BxPc-3, Panc-1, and Mia PaCa-2 with endogenous EphA2 molecule expression, were analyzed through flow cytometry to determine the binding reactivity of indicated scFvs. Freshly prepared cancer cells were harvested and washed twice with PBS. Then, individual scFv was added and incubated at room temperature for 1 h. Bound scFv was visualized using goat anti-chicken light chain antibodies and donkey anti-goat antibodies conjugated with fluorescein isothiocyanate (FITC; Jackson ImmunoResearch Laboratories). An irrelevant scFv was used as the negative control, and commercially available goat anti-EphA2 antibodies were used as the positive control (R&D Systems) in the assay. The results were analyzed using a FACS can flow cytometer (BD Biosciences, Systems and Reagents).
To detect the binding specificity of scFv, 293T cells were transformed with EphA1-A8 plasmids individually for overexpression of different EphA molecules. The cell line was freshly prepared and washed with FACS buffer (2% FBS in PBS). The cells were seeded at 1 × 105 cells/well into a 96-well U-bottom plate and incubated with scFv for 1 h at 4°C. After the plate was washed with FACS buffer, the anti-hemagglutinin (HA) antibody was added for scFv binding detection (scFv was fused with a HA tag) and subsequently developed using an FITC-conjugated secondary antibody. Finally, the cell binding signal was analyzed using a FACS can flow cytometer.
Cell proliferation assay
PAAD cell proliferation was measured using a 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) Cell Proliferation Assay Kit (Promega). The cells were seeded in a 96-well culture plate at a density of 5000 cells/well for attachment. Then, scFv at various concentrations was added to the cell culture and incubated for 5 days. Finally, MTS and phenazine methosulfate solutions were added and incubated for 90 min for development. After the SDS reagent was added to stop the reaction, the absorbance of each well was measured by determining the OD at 490 nm.
Cell migration and scratch wound healing assay
PAAD cells were seeded at 5 × 104 cells/well in a 24-well Transwell cell migration plate (Corning) and incubated with scFv for 2 days. In the assay, recombinant ephrin-A1 (Sino Biological) was added as a positive control. After scFv treatment, the cells were fixed with frozen 100% methanol for 10 min and stained with 0.01% crystal violet for 1 h at room temperature. After the pate was washed with ddH2O, the upper-layer cells were removed using cotton swabs. Cell staining was imaged using a microscope and analyzed using ImageJ.
For the scratch wound healing assay, PAAD cells were seeded in a 6-well culture plate. The seeded cells in the well were scratched with a pipette tip to simulate a wound. After treatment with scFv and incubation for 36 or 72 h, the cells were imaged using a microscope. The wound areas were analyzed using ImageJ.
Molecule signaling
To determine molecule signaling in BxPc-3 and Mia PaCa-2 cells, the cells were cultured in a 6-well culture plate and treated with scFv antibodies at the indicated concentrations for 24 h. The cells were collected and lysed using lysis buffer [50 mM Tris–HCl (pH 7.5), 50 mM NaCl, 5 mM ethylenediaminetetraacetic acid, and 1% Triton X-100], and a mixture of proteinase inhibitors (Roche Applied Science) was added. The protein concentration of the cell lysate was measured through the Coomassie Plus (Bradford) Protein Assay (Thermo Fisher Scientific). Samples were run on reducing SDS-PAGE for Western blotting analysis and were detected using antibodies against p-EphA2, EphA2, p-AKT, AKT, p-ERK, ERK, p-FAK, FAK, p-STAT3, STAT3 (Cell Signaling Technology), and β-actin (GeneTex).
Antibody internalization assay
BxPc-3 cells were seeded on cover glasses placed in the wells of a 6-well culture plate. The BxPc-3 seeded glass slides were incubated with ephrin A1-Fc (Sino Biological) or IgG hSD5 for 1 h at 37°C or 4°C. After washing with PBS, the cells were fixed with 100% ice methanol for 10 min. Next, the cells were stained with an FITC-conjugated anti-human Fc antibody and were subsequently mounted with ProLong Diamond Antifade Mountant comprising 4’,6-diamidino-2-phenylindole for nuclear counterstaining (Invitrogen). The cells were imaged using a confocal microscope (Leica Microsystems).
Tumor xenograft model
The freshly prepared BxPc-3 and Mia PaCa-2 cancer cells were harvested during the log growth phase and resuspended in PBS for tumor implantation. Each NOD/SCID mouse was subcutaneously inoculated with cancer cells (5 × 106 to BxPc-3 and 1 × 107 to Mia PaCa-2) for tumor formation. The tumor size was measured twice weekly, and the volume was calculated as follows: V = 0.5lw2, where l = the length and w = the width. When the tumor size was approximately 100 mm3, animals were divided into groups that received (a) vehicle alone through intravenous injection (i.v.) once weekly (qwk), (b) control human IgG1 at 20 mg/kg through i.v. qwk, (c) and (d) hSD5 IgG1 at 2 or 20 mg/kg through i.v. qwk, (e) and (f) gemcitabine at 20 or 100 mg/kg through i.v. twice weekly (biw), or (g) hSD5 IgG1 at 2 mg/kg through i.v. qwk combined with gemcitabine at 20 mg/kg through i.v. biw. At the end of the experiment, the antitumor effects were quantified by dividing the tumor volumes in the treatment groups by those in the control groups and multiplying them by 100 to represent tumor growth inhibition (TGI; %). The mice were also examined frequently for overt signs of adverse drug-related side effects.
Immunohistochemical staining
The pancreatic tissue microarray slide (US Biomax, PA483e) was used to detect and analyze the EphA2 expression of clinical samples. In the xenograft animal model, the excised BxPc-3 and Mia PaCa-2 tumors were fixed in formalin, embedded in paraffin, and sliced for immunohistochemical staining (IHC). Commercial antibodies (Cell signaling, Dako; Agilent Technologies; and Abcam) were used for staining the EphA2 molecule, cell proliferation marker Ki-67, and apoptosis marker cleaved caspase 3. The effects of staining were observed using a Zeiss Axioskop-2 microscope (Carl Zeiss).
Interaction residue definition
We used peptide enzyme-linked immunosorbent assay (ELISA) to identify the designed epitope on EphA2; the BSA-conjugated peptides EphA2pep_P1 (BSA-CGGGWDLMQNIMNDMPIYMYSV) and EphA2pep_P2 (BSA-CGGGGGGSVSSDFEARHV) each represent the two segments of the linear epitope designed on EphA2. EphA2pep_P1P2 (BSA-CGGGWDLMQNIMNDMPIYMYSVGGGGGGSVSSDFEARHV) represents the two linear epitope sequences connected by a linker. These peptides were synthesized and conjugated with BSA (Kelowna International Scientific). The BSA-conjugated peptides were individually coated on a 96-well microplate at 4°C overnight. After the wells were blocked with 3% BSA, IgG hSD5 was added and incubated. Next, an HRP-conjugated anti-HA tag antibody (Cell Signaling Technology) was used to detect bound scFv. Finally, the TMB substrate was added for development, and the reaction was stopped by adding 1 N HCl. Absorbance was measured by determining the OD at 450 nm.
A dot blot assay was used to detect the binding of IgG hSD5 to the synthesized peptides; 1 mL of individual peptides (1 mg/mL; in triplicate) were dropped on the NC membrane and maintained at RT for complete absorption. Blocking with 3% BSA was performed at RT for 1 h. Then, IgG hSD5 (10 μg/mL) was added, and the reaction was allowed to proceed for 1 h at RT. After the membrane was washed, the HRP-conjugated anti-HA tag antibody was added, and the reaction was allowed to proceed for 1 h at RT. Lastly, DAB was used to initiate the coloration reaction.
Statistical analysis
The data are presented as mean ± standard error of the mean and were analyzed using GraphPad Prism (GraphPad Software). Statistical comparisons between groups were performed using one-way analysis of variance, which was followed by a post hoc Tukey’s honest significant difference test. P values lower than 0.05 were considered significant.