Systems vaccinology and big data in the vaccine development chain

Raeven, René H. M.; van Riet, Elly; Meiring, Hugo D.; Metz, Bernard; Kersten, Gideon F. A.

In addition, the opportunity of sorting specific subsets of cells not only as a population, but also as single cells, in combination with high-throughput analysis of the isolated cells, added yet another dimension. Lymphocyte epitope specificity necessarily is extremely diverse to fight the wide array of possible pathogens and is accomplished by randomness through several recombinatorial events and additional random changes during lymphocyte ontogeny. For example, the number of different antibodies human B-cells can produce, outnumbers the B lymphocytes (~10 11 ) in the human body. 55 High-throughput single-cell analysis enabled detailed interrogation of these broad B-cell and T-cell repertoires. 56 These techniques also revealed that priming might not always be predictive, as preferential expansion of B-cells and T-cells also plays an important role. 57 This illustrates that enhanced understanding of lymphocyte responses not only leads to identification of novel early markers for efficacy of vaccines, but is also useful for their evaluation. Hypotheses with respect to B-cell and T-cell epitopes can be derived from MS-based studies as described in the former paragraph. Moreover, current knowledge with respect to HLA specificity has also enabled the prediction of T-cell epitopes in silico, decreasing the time needed for analysis. 58 As B-cell epitopes are often conformational, current knowledge does not yet enable in silico predictions to the same extent as for T-cells. For B-cell epitope analysis of complex multi-protein vaccines, antibody-antigen binding can be investigated using two-dimensional gel electrophoresis with Western blotting to pinpoint immunogenic antigens. 59 Subsequently, peptide arrays can be applied to investigating the immunodominant epitopes of these discovered antigens. 60 The ability to isolate single antibody-producing B-cells and subsequent DNA sequencing of immunoglobulin genes in high-throughput settings (Ig-seq) has greatly impacted the depth of understanding with respect to the antibody repertoire. 55 Single-cell sorting in combination with B-cell cloning has enabled the isolation of specific antibodies able to neutralize pathogens, including rare antigens with characteristics that are of special interest, such as antibodies that are broadly cross-reactive among highly variable viruses by binding to conserved regions. This was, for example, found for influenza hemagglutinin (HA) subtypes upon infection as well as vaccination. [61] [62] [63] [64] In general, this has shifted the focus from the most immunogenic epitopes to the more conserved regions. However, it has proved challenging to design vaccines that induce strong responses against these regions. Challenges with respect to design of vaccines inducing such broadly neutralizing antibodies for HIV and influenza virus were extensively reviewed by Corti and Lanzavecchia. 65 For example, other regions might need to be removed or deimmunized and the conserved epitopes might not be easily accessible, preventing the vaccine-induced antibodies from binding to the natural target. Another point of attention is that a focus on increased immunogenicity should not lead to a decrease in safety. For example, antibodies with long or charged CDR-H3 regions enable binding to occluded sites on pathogens and mediate pathogen neutralization but are also more likely to be autoreactive. 55 IgG antibody levels have served as correlates of protection for traditional vaccines, 66