E; for the PAP1 and PAP2 antisera, the same epitope was

E; for the PAP1 and PAP2 antisera, the same epitope was recognized. This result is not in contradiction with the previously observed fraction of antibodies that recognized linear epitopes. It was shown that less than 2 of the antibodies raised against the cytochrome c could also recognize the synthetic peptides. The authors concluded that linear epitopes were rare in the case of small, globular, and conformationally stable proteins. The inability of the method to identify the PSA protein which was also used for immunization can be explained by the absence of the response against the linear epitopes of the PSA protein, which is shorter than the PAP protein. We think that if the immune response in mice were to be directed against 2 or more major linear epitopes of the PAP, the PAP protein would be ranked first with a big lead over the other proteins, which were ranked higher mainly due to a shorter size than that of the PAP protein. Although the SAS has been designed for identifying proteins with multiple epitopes recognized by serum antibodies, it appears that aSerum Antibody Repertoire ProfilingFigure 4. Epitope mapping for human PAP-specific antibodies from four immune sera samples. The reactivity of 4 mouse PAP-specific immune sera (PAP1, PAP2, PAP3 and PAP4) was tested by ELISA using a library of overlapping 20-mer peptides that span the entire amino acid ?sequence of human PAP. Base1 and base 2 samples derived from naive mice served as negative controls. The results for the PAP protein region corresponding to amino acids 193?62 are shown. doi:10.1371/Epigenetic Reader Domain journal.pone.0067181.glarge number of different peptides that have matches to a single epitope may be sufficient for identifying a protein as a Epigenetics candidate antigen. However, when only a single major epitope is detected on the candidate protein, the possibility that the protein is identified due to a chance can not be excluded. Based on the analysis of the PAP3 serum sample we had to choose another protein, and not the PAP protein as the first candidate for the target of the immune response (Table 1). Even when binding of a protein to serum antibodies is confirmed by Western blot, as was the case with the CPA3 protein and the melanoma patient’s serum antibodies, this binding does not necessary mean that the immune response was 23148522 directed against this protein, but could be attributed to the cross reactivity. It is possible that the peptide sequence recognized by serum antibodies of the melanoma patient on the CPA3 protein is the mimic of a conformational or carbohydrate epitope on the other human, viral or bacterial protein, which may represent the unknown real target of the humoral immune response. This limitation of the SAS method is shared with the other methods of serum antibody repertoire profiling which are based on using the cDNA expression libraries, such as SEREX [9]. When we analyzed the reactivity of the melanoma serum sample against the next ranked highest after the CPA3 protein, the serum antibody did not detect the corresponding band on the western blot. The absence of the specific signal for the protein on the western blot does not necessary mean the absence of autoantibodies against this protein. It can 1676428 be explained by the much higher sensitivity of the SAS over the Western blot. Thedetection of the immunoreactivity in the SAS is based on sequencing of the PCR amplified DNA fragment coding for the peptide that binds to antibodies. The method can detect even a single peptide t.E; for the PAP1 and PAP2 antisera, the same epitope was recognized. This result is not in contradiction with the previously observed fraction of antibodies that recognized linear epitopes. It was shown that less than 2 of the antibodies raised against the cytochrome c could also recognize the synthetic peptides. The authors concluded that linear epitopes were rare in the case of small, globular, and conformationally stable proteins. The inability of the method to identify the PSA protein which was also used for immunization can be explained by the absence of the response against the linear epitopes of the PSA protein, which is shorter than the PAP protein. We think that if the immune response in mice were to be directed against 2 or more major linear epitopes of the PAP, the PAP protein would be ranked first with a big lead over the other proteins, which were ranked higher mainly due to a shorter size than that of the PAP protein. Although the SAS has been designed for identifying proteins with multiple epitopes recognized by serum antibodies, it appears that aSerum Antibody Repertoire ProfilingFigure 4. Epitope mapping for human PAP-specific antibodies from four immune sera samples. The reactivity of 4 mouse PAP-specific immune sera (PAP1, PAP2, PAP3 and PAP4) was tested by ELISA using a library of overlapping 20-mer peptides that span the entire amino acid ?sequence of human PAP. Base1 and base 2 samples derived from naive mice served as negative controls. The results for the PAP protein region corresponding to amino acids 193?62 are shown. doi:10.1371/journal.pone.0067181.glarge number of different peptides that have matches to a single epitope may be sufficient for identifying a protein as a candidate antigen. However, when only a single major epitope is detected on the candidate protein, the possibility that the protein is identified due to a chance can not be excluded. Based on the analysis of the PAP3 serum sample we had to choose another protein, and not the PAP protein as the first candidate for the target of the immune response (Table 1). Even when binding of a protein to serum antibodies is confirmed by Western blot, as was the case with the CPA3 protein and the melanoma patient’s serum antibodies, this binding does not necessary mean that the immune response was 23148522 directed against this protein, but could be attributed to the cross reactivity. It is possible that the peptide sequence recognized by serum antibodies of the melanoma patient on the CPA3 protein is the mimic of a conformational or carbohydrate epitope on the other human, viral or bacterial protein, which may represent the unknown real target of the humoral immune response. This limitation of the SAS method is shared with the other methods of serum antibody repertoire profiling which are based on using the cDNA expression libraries, such as SEREX [9]. When we analyzed the reactivity of the melanoma serum sample against the next ranked highest after the CPA3 protein, the serum antibody did not detect the corresponding band on the western blot. The absence of the specific signal for the protein on the western blot does not necessary mean the absence of autoantibodies against this protein. It can 1676428 be explained by the much higher sensitivity of the SAS over the Western blot. Thedetection of the immunoreactivity in the SAS is based on sequencing of the PCR amplified DNA fragment coding for the peptide that binds to antibodies. The method can detect even a single peptide t.

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