Abstract
The immune system produces a diverse repertoire of immunoglobulins in response to foreign antigens. During B-cell development, VDJ recombination and somatic mutations generate diversity, whereas selection processes remove it. Using both proteomic and NGS approaches, we characterized the immune repertoires in groups of rats after immunization with purified antigens. Proteomics and NGS data on the repertoire are in qualitative agreement, but did show quantitative differences that may relate to differences between the biological niches that were sampled for these approaches. Both methods contributed complementary information in the characterization of the immune repertoire. It was found that the immune repertoires resulting from each antigen had many similarities that allowed samples to cluster together, and that mutated immunoglobulin peptides were shared among animals with a response to the same antigen significantly more than for different antigens. However, the number of shared sequences decreased in a log-linear fashion relative to the number of animals that share them, which may affect future applications. A phylogenetic analysis on the NGS reads showed that reads from different individuals immunized with the same antigen populated distinct branches of the phylogram, an indication that the repertoire had converged. Also, similar mutation patterns were found in branches of the phylogenetic tree that were associated with antigen-specific immunoglobulins through proteomics data. Thus, data from different analysis methods and different experimental platforms show that the immunoglobulin repertoires of immunized animals have overlapping and converging features. With additional research, this may enable interesting applications in biotechnology and clinical diagnostics.
Highlights
The basic understanding of the molecular biology that leads to diversity in the adaptive immune response emerged around 1980 [1], an effort that was awarded with a Nobel prize for Physiology and Medicine for Tonegawa
The immunizations and proteomics dataset were described in earlier work [10]
The data presented combine NGS and proteomics analysis to show that immune responses result in antibody sequence fragments that are shared among subjects exposed to the same immunogen
Summary
The basic understanding of the molecular biology that leads to diversity in the adaptive immune response emerged around 1980 [1], an effort that was awarded with a Nobel prize for Physiology and Medicine for Tonegawa. It is challenging to obtain a sample for sequencing that properly reflects the repertoire of antibody proteins that is present in the serum, and even more the repertoire of an antigen-specific subset of sequences. Distinctions have been found between the B-cell receptor repertoire and the plasma cell repertoire that drives immunoglobulin expression [3] Another challenge is the tissue niche that is sampled for obtaining sequence information. Antibody proteins can be collected from serum and affinity-enriched in order to study an antigen-specific subset of molecules. For these reasons, we here study the immune repertoire with a combination of proteomics and NGS. The techniques were already combined successfully in the past, and can help provide unique but not always consistent views on the repertoire [4,5,6,7,8]
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