Immune Responses Are Characterized by Specific Shared Immunoglobulin Peptides That Can Be Detected by Proteomic Techniques
peer-reviewed · Journal of Biological Chemistry · 2010
| Date | 2010-09-01 |
| Type | peer-reviewed |
| Venue | Journal of Biological Chemistry |
| Publisher | American Society for Biochemistry and Molecular Biology |
| Contribution | downstream-application |
| DOI | 10.1074/jbc.M110.139071 |
Abstract
In the adaptive immune response, immunoglobulins develop that bind specifically to the antigens to which the organism was exposed. Immunoglobulins may bind to known or unknown antigens in a variety of diseases and have been used in the past to identify novel antigens for use as a biomarker. We propose that the immunoglobulins themselves could also be used as biomarkers in antibody-mediated disease. In this proteomic study, rats were immunized with one of two purified antigens, and immunoglobulins from pre- and postimmune sera were analyzed with nano-LC coupled mass spectrometry. It was found that the two treatment groups could be distinguished based on cluster analysis of the immunoglobulin peptides from the immune sera. In addition, we identified 684 specific peptides that were differentially present in one of the two treated groups. We could find an amino acid sequence for 44% of the features in the mass spectra by combining database-driven and de novo sequencing techniques. The latter were essential for sequence identification, as the more common database-driven approach suffers from a poor representation of immunoglobulins in the available databases. Our data show that the development of immunoglobulins during an immune response is not a fully random process, but that instead selection pressures exist that favor the best binding amino acid sequences, and that this selection is shared between different animals. This finding implies that immunoglobulin peptides could indeed be a powerful and easily accessible class of biomarkers.
Methods and tools
- Immunoglobulin peptide biomarker profiling: Immunoglobulin peptides themselves used as biomarkers of an immune response, rather than the antigens they bind. Rats were immunised with one of two purified antigens and immunoglobulins from pre- and post-immune sera were profiled by nano-LC on an LTQ-Orbitrap with top-5 data-dependent fragmentation, giving 684 peptides differentially present between the treatment groups and cluster separation of the two. Sequences were obtained for 44% of spectral features by combining Mascot database search with de novo sequencing in PEAKS Studio 5.1, merged in Progenesis, which keeps the best-scoring sequence per feature. The authors state the de novo half was essential, because immunoglobulins are poorly represented in sequence databases. The shared peptides found across animals indicate that repertoire development is not fully random but under selection pressure favouring the best-binding sequences.
- PEAKS: Commercial DP-based de novo