Background
According to the Network Theory of Niels Jerne, the immune system is a network of interacting idiotypes that is involved in the regulation of immune responses [
1]. Anti-idiotypic (Ab2) antibodies are a special set of antibodies that can react with idiotopes, which represent unique antigenic determinants on the surface of an antibody. Each antibody constitutes a small set of idiotopes that form its own idiotype. Private idiotopes have been shown to be associated with the complementarity-determining regions (CDRs), which, in addition to various rearrangements of V-(D)-J gene segments, also reflect random somatic mutations and/or N-region additions with a low probability of repetition in another individual. Unlike private idiotopes, recurrent idiotopes are encoded by germline genes, which can generally tolerate some somatic mutations without the loss of the original idiotope [
2]. A single idiotope can stretch over a part of the CDR and a part of the framework region, as well as over both the light and heavy chain residues.
Ab2 antibodies can be classified into three distinct groups: the Ab2α antibody group are conventional antibodies that recognize idiotopes distinct from the antigen-combining site on primary Ab1 antibodies; Ab2β antibodies are internal image antibodies that recognize epitopes within the antigen-combining site and that resemble the nominal antigen (internal image); and Ab2γ antibodies recognize epitopes within the antigen-combining site, but do not resemble the nominal antigen [
3].
The most intriguing group of Ab2 antibodies are those of Ab2β, the internal image antibodies, which are directed against the binding site of the eliciting antibodies and can, in their paratope, structurally and/or functionally mimic the original antigen, or more precisely, the epitope of the original antigen [
4‐
8]. This feature has led to the idea of using internal image antibodies as surrogate antigens for the development of active vaccines. Such an approach is especially useful when the hypothetically protective antigens are infectious, toxic or difficult to isolate and purify, as is the case in prion disease vaccine development.
Prion diseases, which are also known as transmissible spongiform encephalopathies (TSEs), are a group of incurable, fatal neurodegenerative diseases that affect humans and animals [
9,
10]. According to the widely accepted "protein only" hypothesis proposed by Stanley B. Prusiner, TSEs are caused by misfolding of the normal cellular prion protein (PrP
C) into the protease-resistant isoform, PrP
Sc, which then accumulates in the central nervous system [
10,
11]. Since the epidemic of bovine spongiform encephalopathy (BSE) in the nineties and the transmission of the disease to humans as variant Creutzfeldt-Jakob disease (vCJD) [
12,
13], significant scientific resources have been devoted to improve our understanding of prion biology. Interestingly, to date, it has not been possible to detect a significant anti-PrP
Sc immune response during the course of prion diseases [
10,
14,
15]. Similar difficulties emerge with attempts to experimentally evoke a protective anti-PrP
Sc immune response in wild-type animals, when the recombinant prion protein or peptides derived from the amino-acid structure of the prion protein are used as antigens for immunization [
16‐
21]. Since the prion protein is a highly conserved ubiquitous protein, it induces strong B-cell and T-cell immune tolerance when introduced into an organism [
20,
22].
As an alternative to conventional active anti-prion vaccine development, the Ab2 approach offers another way to overcome the unresponsiveness of the immune system. For the development of Ab2 antibodies that mimic the PrP
Sc-specific epitope, a PrP
Sc-specific antibody is a prerequisite. In our previous studies, we described and characterized V5B2, a PrP
Sc-specific monoclonal antibody, and indicated its potential applicability for diagnostic purposes [
23,
24]. Based on biophysical studies, it has been proposed that V5B2 recognizes an epitope on PrP
Sc that is similar or identical to the conformation of the P1 peptide in solution (predominantly a dimeric/oligomeric form) and in fibril-like aggregates, both of which differ from the conformation of the corresponding region in PrP
C [
25].
According to the internal image phenomena, Ab2β antibodies against the V5B2 paratope would carry the PrPSc-specific epitope image in their antigen-combining site, thereby providing an insight into its structure and maybe even serving as a tool for idiotypic vaccine studies.
The aim of this study was thus to investigate the applicable ways to induce an anti-idiotypic response to the PrPSc-specific monoclonal antibody in xenogeneic and syngeneic experimental systems, and to define the preparation of Ab2 monoclonal antibodies with well-defined strategies for immunization, selection and subsequent characterization.
Discussion
Over the past decade, the anti-idiotypic vaccine approach has been successfully used for various aspects of vaccinology, such as autoimmune diseases, enteric intoxification, rejection of allografts, allergic diseases, foetal immunity regulation, and in particular, tumour immunotherapy [
27]. This is the method of choice when the surrogate protective antigens are carbohydrate moieties or glycoproteins, when protective antigens are difficult to isolate and purify, when synthetic peptides cannot form the tertiary structure present in protective antigens, and when infectious agents with unpredictable effects are used [
28‐
31]. Some of the properties listed also hold true for the pathological form of the prion protein. Induction of protective anti-prion immune response in wild type animals is extremely difficult, because of the host tolerance to endogenous PrP
C (for review see [
21]). To date, no entirely successful attempt of active immunization in the field of TSE has been published, although some hypothetically protective target sites on the prion protein have been proposed [
18,
19]. However, to our knowledge, no method has been widely accepted. Anti-idiotypic vaccines would therefore represent a novel approach for prion disease prevention and treatment.
Results of passive vaccination and cell-culture studies indicate that only monoclonal antibodies that bind to the membrane PrP
C are efficient in blocking prion propagation and pathogenesis [
32‐
35]; at the same time, it has been shown that monoclonal antibodies that recognized both PrP
C and PrP
Sc, blocked PrP
Sc accumulation
in vitro even more efficiently than monoclonal antibodies specific for PrP
C only [
36]. However, the cross-linking of PrP
C in vivo caused extensive neuronal damage [
37] and in our opinion this finding needs to be noted when potent PrP
C-specific antibodies are to be induced or introduced for treatment or prophylaxis purposes. Therefore an approach to exclusively target PrP
Sc would avoid all of the problems regarding the binding of antibodies to PrP
C and the resultant cessation of normal PrP
C function.
To directly target the pathological isoform in the development of an anti-idiotypic vaccine, a PrP
Sc-specific antibody is a prerequisite. However, only a few PrP
Sc-specific antibodies have been reported [
23,
24,
38‐
40], and due to their individual characteristics, not all of them are suitable for this purpose.
The V5B2 monoclonal antibody that was previously described by our group is a potent PrP
Sc-specific antibody that reacts with the native PrP
Sc deposits in immunohistochemistry [
24]. This thus represents an appropriate candidate to preserve the information of the native PrP
Sc-specific epitope in its antibody-combining site. In the present study, the main ways of producing Ab2 antibodies against the PrP
Sc-specific antibody have been studied in two experimental models: in xenogeneic and syngeneic systems.
Mammalian proteins are highly immunogenic in chickens. As expected for xenogeneic immunization, the antibody titre in the antiserum was high. Although the immune response was expected against the whole immunoglobulin molecule, anti-idiotypic response was surprisingly potent, with the ability to totally block the binding of V5B2 to the P1 peptide or PrPSc. However, despite promising results after testing the immune sera and affinity purified Ab2 IgY antibodies, we were not able to isolate stable chicken hybridoma cell lines that retained the antibody production. The main reason appears to be that to date chicken hybridoma technology has been poorly studied in comparison to mouse hybridoma technology; the system therefore still needs to be optimized for use as a routine experimental procedure.
In our syngeneic studies, the antigen (Ab1 V5B2) was actually a self-protein, produced in a BALB/c mouse and injected into an inbred BALB/c mouse with virtually the same genetic background, and therefore self-tolerance to the whole constant part of the immunoglobulin was expected. Groups of BALB/c mice were immunized with 3 different forms of the same antigen. Whole IgG V5B2 was the original and the least chemically treated molecule used for immunization. It is a relatively large molecule, predominantly composed of the self constant region, with only a minor part being immunogenic in a syngeneic experimental system. Although the immune tolerance to the whole constant part of the immunoglobulin molecule was expected, we also wanted to assess whether the use of the smaller fragment Fab V5B2, lacking the constant Fc-region, potentiates the immune response to idiotopes. In addition to the whole V5B2 and Fab V5B2, the Fab V5B2, covalently coupled to the highly immunogenic carrier molecule KLH, was used for immunization, to maximize the specific helper T-cell response and to potentiate the immune response against idiotopes on V5B2. Nevertheless, a prominent immune response was achieved with all three antigens. Surprisingly, even though the immune response against the whole IgG V5B2 was relatively strong, the antisera capacity to inhibit the V5B2 binding to the P1 peptide was much lower in comparison to the inhibitory capacity of the antisera obtained by immunization with the smaller fragment, Fab V5B2. Because of the higher molecular weight of the whole IgG V5B2 in comparison to the Fab V5B2, less idiotopes of V5B2 are present per μg of antigen injected in case of the whole IgG. This could contribute to the lower immune response and lower inhibitory capacity of the obtained sera. It is also possible that the immune response was directed predominantly against the glycan moieties of the constant region in case of the whole IgG, as the glycosylation profile of monoclonal antibodies is affected by the cell culture conditions and can differ from the normal antibody glycosylation observed
in vivo [
41]. Based on the observed inhibitory capacity, only the mice immunized with Fab V5B2 and Fab V5B2-KLH were sacrificed for the cell fusion. The resulting hybridoma cell lines produced predominantly IgG Ab2 antibodies, in contrast to other Ab2 antibody studies, where the antibodies were mainly of the IgM class [
4,
5,
42,
43]. The obtained Ab2 antibodies bound Fab V5B2 with a high affinity, characteristic of affinity-matured IgGs.
The main objective in the present study was to select Ab2 antibodies that recognize private idiotopes. Therefore, the selection process included Fab fragments of monoclonal antibodies with the same specificities for the peptide antigen, but with different specificities for the prion protein isoforms. Indeed, the majority of the antibodies used in the negative selection process (Table
1) were directed against the P1 peptide derived from the C-terminal amino-acid sequence of the human prion protein, which can adopt different conformations in solution, and therefore, which can elicit antibodies of different specificities when injected into wild-type mice [
23]. The comparison of the variable region amino-acid sequences of both the light and heavy chains, between antibodies that had been used in the negative selection process and our antigen, Fab V5B2, revealed considerable analogy. The V
H and V
L amino-acid sequences of these antibodies differ only slightly, and most importantly, the differences between these antibodies are predominantly restricted to the CDR regions (Table
2). Nevertheless, all of the Ab2 monoclonal antibodies selected still distinguished between the Fab fragments of these antibodies, which indicated a very precise selectivity of our Ab2 monoclonal antibodies for private idiotopes, most probably restricted to the CDR regions of V5B2. Subsequent
in silico structural modelling of the 5D12-V5B2 complex also revealed the close interaction of both CDR regions (Fig.
5).
Based on the selection process described and the affinities of the Ab2 antibodies for Fab V5B2 as well as their inhibition potential, two Ab2 monoclonal antibodies, 5D12 and 4F8, were selected for further characterization. Since no functional test is available to determine the presence of Ab2 antibodies that bind to the antigen-combining site of a PrP
Sc-specific antibody, at first an ELISA-based inhibition assay was designed to characterize the Ab2 antibody response. Ab2 antibodies in chicken and mouse polyclonal immune sera and Ab2 murine monoclonal antibodies (Figs.
1B, 1C,
2B and
3B) substantially inhibited the binding of Ab1 to the P1 peptide in a dose-dependent manner. This indicated that in agreement with idiotypic network theory, immunization with Fab V5B2 induced Ab2 antibodies, which bear the functional epitope for Ab1 that competes with the original antigen, the P1 peptide, and in turn have to be similar to the P1 peptide structure. The reasons for the stronger inhibition of the polyclonal immune sera in comparison to monoclonal antibodies can be accounted for by the higher antibody concentration, a wider variety of Ab2 antibody specificities, and consequently also a wider variety of target epitopes present in polyclonal preparations.
In addition to the ELISA-based inhibition assay, the competitive immunohistochemistry assay was set up to show that Ab2 antibodies inhibit not only binding of V5B2 to the P1 peptide but also to the original target molecule, PrP
Sc. Indeed, we observed 90% and 50% inhibition of binding of V5B2 to PrP
Sc using high concentrations of 5D12 and 4F8, respectively, whereas the isotype control did not show any significant inhibition at the same concentrations. The inhibition of binding was concentration dependent, which indicates the specificity of the effects seen. Furthermore we saw 88% inhibition with the use of much lower concentrations of polyclonal Ch5 as competitor, again probably due to a wider variety of Ab2 antibody specificities with synergistic effects, present in the polyclonal preparation. The results of the competitive immunohistochemical studies, together with the results of the competitive ELISA, strongly indicate that the selected Ab2 antibodies bind into the V5B2 binding site, thereby hindering the binding of V5B2 to the P1 peptide, and most importantly to the original target, the PrP
Sc molecule. In addition, the structural model of the 5D12-V5B2 complex, obtained by molecular docking, also strongly supports the close interaction of both antibody-combining regions, since the majority of the interacting residues are located in the CDR regions (Figs.
5C, 5D).
Based on previous studies, Ab2 antibodies can resemble the amino-acid sequences of nominal antigens in their variable regions, especially when the nominal antigen is a peptide [
44‐
46]. The P1 peptide motif could be preserved in a single CDR sequence or in a conformational stretch across different CDR loops of a single chain, as well as across different loops of both the heavy and light chains. The latter, i.e. the involvement of different CDR loops of both chains, is also evident from the proposed model of the 5D12-V5B2 complex. The comparison of the 5D12 binding interface to the P1 peptide reveals structural similarities to its C-terminal. This is especially important in the light of our recent unpublished data, which indicate that the C-terminal residues are crucial for the V5B2 binding to the P1 peptide. It is therefore possible that the 5D12 binding surface mimics the crucial part of the P1 peptide and the epitope, unique to the PrP
Sc molecule. Nevertheless, the computer modelling data must be interpreted cautiously; still, the obtained docking model is in agreement with the observed experimental data. The proposed model also achieved an outstanding ranking score using both the surface complementarity and the global energy criteria.
Methods
Animals
Chickens from a divergently selected line (D+) for high body weight [
47] were bred and maintained in the Department of Animal Science at the Biotechnical Faculty, University of Ljubljana. BALB/c mice were bred and maintained in the Animal Facility at the Blood Transfusion Centre of Slovenia. Both groups of animals were handled in accordance with the FELASA recommendations and guidelines.
Cell lines
V5B2 (Ab1), a B-cell hybridoma cell line of BALB/c origin, was generated against the 13-residue synthetic P1 peptide (CITQYERESQAYY), which was derived from the C-terminal α-helix of the human prion protein (amino acids 214–226), coupled to keyhole limpet hemocyanin (KLH) [
24]. The NS1 murine myeloma cell line, the V5B2 hybridoma cell line and all murine hybridoma cell lines prepared in this study were maintained in Dulbecco's modified Eagle's medium (DMEM; ICN Biomedical) supplemented with 13% bovine serum (HyClone), 2 mM L-glutamine (Sigma), 130 μg/μl streptomycin (Sigma) and 100 U/ml penicillin (Sigma) (subsequently referred to as DMEM+). The MuH1chicken myeloma cells and clones obtained by fusion of chicken cells were cultured in Iscove's Modified Dulbecco's medium (Sigma) with addition of foetal bovine serum (HyClone) and gentamycin (Sigma) at final concentrations of 10% and 0.1%, respectively.
Antigens
We prepared three different antigens for the immunization: the whole V5B2 antibody, the Fab fragment of the V5B2 antibody, and the Fab fragment of the V5B2 antibody coupled to KLH. All supernatants from murine hybridoma cells were purified by gravity-flow affinity chromatography on Protein G Sepharose (Amersham) using 0.1 M glycine, pH 2.7, for elution. The Fab fragments were produced by cleaving with immobilized papain (Pierce) and purification on Protein A Sepharose CL-4B (Pharmacia Biotech). The identity and purity of the Fab fractions were determined by indirect ELISA and Western blotting. The Fab fragments of V5B2 were coupled to KLH via 4-maleimidobutyric acid N-hydroxysuccinimide ester (GMBS, Sigma), according to the procedure described by Yoshitake et al. [
48].
Chicken immunization and fusion protocol
Five chickens were immunized intramusculary every 3 weeks with the whole V5B2 monoclonal antibody as antigen. In each immunization, 400 μg of antigen was applied into three places in the breast muscle, in a total volume of 1 ml. For the first immunization, the antigen was mixed with Complete Freund's Adjuvant (1:1 v/v; Sigma), for the second immunization, with Incomplete Freund's Adjuvant (Sigma), and for all of the subsequent immunizations, with physiological saline. After the 4th immunization, the titres of anti-V5B2 antibodies were estimated by ELISA and the two chickens with the highest antibody titres were selected. They received two more boosters of the Fab fragment of V5B2. Three days after the last immunization booster, these chickens were sacrificed, and their blood was collected for the preparation of the polyclonal anti-serum and their spleens were removed for monoclonal antibody production.
The chicken hybridoma cells were produced as described previously [
49,
50]. Briefly, spleen cells from the immunized chickens were fused with the MuH1 chicken myeloma cell line in a ratio of 1:3 using 50% polyethylene glycol. Hybridoma cells were selected while maintaining the cells in medium containing HAT (hypoxanthine, aminopterin, thymidine; Sigma) or HT (hypoxanthine, thymidine; Sigma), at a final concentration of 1%, and ouabain (Sigma), at a final concentration of 20 μM.
Chicken polyclonal antibody affinity purification
Fab V5B2 was covalently immobilized to agarose beads (Pierce) according to the manufacturer protocol. Blood serum from the chicken with the most potent immune response, collected after immunization, was applied to the column with the immobilized Fab V5B2. After extensive washing the bound fraction was eluted using 0.1 M glycine, pH 2.7.
Mouse immunization and fusion protocol
Female BALB/c mice (6–8 weeks old) were immunized with three different antigens: the whole V5B2 antibody, the Fab fragment of the V5B2 antibody, and the Fab fragment of the V5B2 antibody coupled to KLH. Each mouse was immunized subcutaneously with 0.1 mg antigen in Complete Freund's Adjuvant on day 0, and then intraperitoneally with 0.1 mg antigen in Incomplete Freund's Adjuvant on days 14, 28 and 42. On day 52, the mice were bled from the tail vein and the immune sera were collected. A final booster of 50 μg antigen in physiological saline was administered intravenously on day 57, although only into the mice with the highest antibody titres, which were the ones selected as spleen-cell donors for the cell fusion. The mice were sacrificed on day 61, and their spleens were removed. Splenocytes were isolated and fused with mouse NS1 myeloma cells with 50% polyethylene glycol for 3 min, according to standard procedures. Hybridoma cells were selected by maintaining the cells for two weeks in HAT DMEM+ and another week in HT DMEM+ selection medium (DMEM+ supplemented with HAT or HT, respectively). The presence of specific antibodies was determined in supernatants after 10 to 14 days by indirect ELISA. Selected hybridomas were cultured until stable cell lines were established, and then subcloned by limiting dilution, and frozen in liquid nitrogen.
Murine anti-idiotypic monoclonal antibody selection
Microtitre ELISA plates (Nunc) were coated with 50 μl Fab fragment at 1 μg/ml in 50 mM carbonate/bicarbonate buffer, pH 9.6, and incubated overnight at 4°C. The next day, the plates were washed three times with washing buffer (sodium phosphate buffer, containing 150 mM NaCl, 0.05% Tween 20, pH 7.2–7.4) and blocked for 30 min at 37°C with blocking buffer (1% BSA in washing buffer). The plates were washed again and then incubated with the following primary antibodies: polyclonal immune sera, cell culture supernatant, or purified monoclonal antibodies, all diluted in blocking buffer, for 1.5 h at 37°C. After washing, the plates were incubated with a secondary goat anti-mouse IgG (γ-chain specific) conjugated to horseradish peroxidase (HRP, Sigma), diluted 1:3,000 in blocking buffer, and incubated again for 1.5 h at 37°C. After incubation with the 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS, Sigma) substrate in citrate-phosphate buffer, pH 4.5, for 20 min at 37°C, the reaction was measured spectrophotometrically at 405 nm with a microtitre plate reader.
The 5D12 and 4F8 clones were chosen for further experiments, as they consistently produced the highest titre antibodies, as determined by indirect ELISA. The 6C5 murine IgG1 monoclonal antibody, specific for antigen B of the human polysaccharide blood group system AB0, served as an isotype negative control monoclonal antibody throughout the study.
Determination of affinity constants
The affinity constants (
Kaff) of the Ab2 monoclonal antibodies were determined in a non-competitive immunoassay [
51]. Briefly, an ELISA plate (Nunc) was coated overnight with Fab V5B2 at three different concentrations: 5 μg/ml, 2.5 μg/ml and 1.25 μg/ml. The Ab2 monoclonal antibodies were applied at three-fold serial dilutions, with concentrations ranging from 9 μg/ml down to 12 ng/ml. The incubations with the secondary antibody and the ABTS substrate were performed as described above.
Competitive ELISA
Chicken immune sera
For the competition studies, ELISA plates (Nunc) were coated with 0.5 μg/ml P1 peptide (JPT) overnight. The next morning, the plates were washed and blocked as described above. Then 1 μg/ml V5B2 was separately mixed with different dilutions of chicken immune sera and incubated for 1 h at 37°C prior to application to the blocked ELISA plate, with a further incubation for 90 min at 37°C. This step was followed by washing and the addition of a secondary goat anti-mouse Fab-specific HRP conjugate (Sigma) diluted 1:5,000 in blocking buffer, with a further incubation for 1.5 h at 37°C. Detection was performed as above, and the percentage of specific inhibition was calculated relative to buffer controls and by taking the optical density of the well containing no competitor as 100%.
Mouse immune sera, mouse monoclonal antibodies and purified chicken polyclonal antibodies
As described above, ELISA plates were coated overnight at 4°C with 0.5 μg/ml or 0.25 μg/ml P1 for testing immune sera and purified antibodies, respectively. The next morning, the plates were washed and blocked with blocking buffer. V5B2 conjugated to HRP (V5B2-HRP), diluted 1:1,500, was separately mixed with different dilutions of mice immune sera, Ab2 monoclonal antibodies, purified chicken polyclonal antibodies (subsequently called Ch5) or an isotype control antibody, and incubated for 1 h at 37°C prior to application to the blocked ELISA plate and incubation for another 1 h at 37°C. After washing, the detection step was carried out as described above, and again, the percentage of specific inhibition was calculated relative to buffer controls and by taking the optical density of the well containing no competitor as 100%.
Immunohistochemistry
Tissue samples
Adjacent sections of paraformaldehyde-fixed, paraffin-embedded human cerebellar tissue samples from a patient with confirmed sporadic CJD (sCJD) with synaptic prion deposition and primitive plaques (Val/Val on codon 129 of the prion protein gene) were used in the study, which were obtained from the archive of the Institute of Pathology, Faculty of Medicine, University of Ljubljana. The tissue samples were immersed in 96% formic acid for 1 h after fixing in paraformaldehyde. The 5-μm-thick sections were used immediately after deparaffination and the antigen retrieval procedure involving 30 min autoclaving at 121°C in distilled water and then a 5-min incubation in 96% formic acid, which is the standard recommended pretreatment for optimal PrP
Sc immunodetection in tissue sections [
52].
Competitive immunohistochemistry
Direct immunohistochemical detection of prion deposits was performed with V5B2-HRP and using 3,3-diaminobenzidine as chromogen (Sigma). V5B2-HRP was diluted 1:100 in a vehicle solution containing 1% BSA (Sigma) and 0.04% Triton X-100 (Sigma) in phosphate buffer, pH 7.2. Competitors at stated concentrations were preincubated with V5B2-HRP in the same solution for 12 h at 4°C before applying the solution onto tissue sections, which were then incubated overnight in a moist chamber at room temperature. The sections were then rinsed thoroughly (10 × 10 min) and developed in chromogen for 5 min. Simultaneously processed sections incubated only in vehicle buffer solution and developed in chromogen served as a negative control.
Image collection and analysis
Photomicrographs were taken using 20 × objective on a Nikon Eclipse E600 microscope equipped with a Nikon DXM 1200 digital camera, and connected to a personal computer station running NIS-D software. Every section was photographed at 5 locations, chosen to always reveal cerebellar cortical layers in balanced proportions.
Images of the brown immunoreactive product were smoothed with Gaussian kernel (1 pixel radius), inverted and colour-hue adjusted (the hue was rotated by 272°) to transform the brown immunoreactive product on a white background to a green signal on a black background. All of the image pre-processing was accomplished in Adobe Photoshop CS3 (Adobe, San Jose, CA, USA) using an automated action. All further analysis was conducted on the green signal intensity only. To establish a baseline from which signal was estimated, a threshold was chosen at which only 0.1% of the negative control image surface remained above threshold. All images were then thresholded (all pixels with intensity below the threshold were set to 0) and the mean signal value for each image was computed. To remove the effects of the remaining noise, the mean signal value of negative control images (n = 5) was subtracted from each image value. Finally, to express the signal intensities as percentages of the positive control intensity, the mean intensity values were divided by the mean positive control intensity (uncompeted immunohistochemistry with V5B2-HRP) and multiplied by 100. All of the image intensity analysis was carried out using Matlab (Mathworks, Natick, MA, USA).
Statistical analysis of immunohistochemical data
The differences in effects of different competitor molecules were estimated using one-way ANOVA. To test for significant differences in intensities between test samples and the positive control, a one-tailed t-test for independent samples with unequal variances was used. Based on the number of tests, a Bonferroni corrected p value of 0.004 was chosen as the threshold for statistical significance.
Polymerase chain reaction amplification and sequence analysis of heavy and light chains
Amplification and sequencing of monoclonal Ab2 antibody heavy and light chains were performed as described by Koren et al. [
53]. All of the nucleotide sequence analyses and translations were carried out using the BioEdit programme [
54] or the ExPASy proteomics server [
55]. All of the immunoglobulin gene analyses were performed using IMGT, the international ImMunoGeneTics information system [
56].
Antibody modeling and molecular docking
The variable regions of V5B2 and 5D12 were modeled following the procedure described by Morea et al. [
57]. For V5B2, relevant chains from Protein Data Bank (PDB) structures 1KB5 and 1NBV were used as the light and heavy chain variable regions (V
L and V
H) templates, showing 94.5% and 92.7% similarity to the corresponding V5B2 sequences, respectively. The H3 hypervariable loop was modeled separately, using H3 loop from the PDB structure 1VFA as the closest match of the same length and torso conformation, with 53.8% similarity. For 5D12, PDB structures 2PCP, 1FSK and 1DBA were used as the templates for V
L, V
H and H3 loop, with the similarities to the corresponding 5D12 sequences being 97.5%, 85.9% and 73.3%, respectively. All similarities were calculated using the BLOSUM62 matrix All structure manipulations were carried out in Swiss-PdbViewer [
58] and UCSF Chimera [
59].
The 5D12 and V5B2 variable region models were docked using Patchdock molecular docking algorithm based on shape complementarity principles [
60], with the antibody-antigen complex type option enabled. The 5D12 model was specified as the antibody and the V5B2 model as the antigen. One hundred best ranking solutions were further refined and scored according to a binding energy function using the Firedock algorithm [
61].
Authors' contributions
ACV carried out the murine immunizations, antibody selection and characterization, participated in the design of the study and drafted the manuscript. MB participated in the design of competitive immunohistochemical studies and carried out the image collection, analysis and statistical analysis of immunohistochemical data. TV carried out the immunohistochemical study and participated in the design of the study. SK carried out the antibody modelling and molecular docking. MN carried out the chicken immunizations and cell fusion experiment. MP participated in evaluation of immunohistochemical results. VCS conceived of the study, and participated in its design and coordination and helped to draft the manuscript. All authors read and approved the final manuscript.