Herein we present a meta-analysis of epitope data related to the Plasmodium genus. We anticipate that this analysis will help establish a broader picture of malaria-related epitope data with relevance for the identification of epitopes and antigens associated with protective immunity, assisting in vaccine design and development, and for the characterization of immune response to Plasmodium variant strains. The results of this analysis are also relevant for the identification of knowledge gaps and areas of further investigation in the field.
More than 1500 different epitope structures are described in the literature. About half are T cell epitopes, and CD4 epitopes out-number CD8 epitopes 4 : 1. This may be a reflection of predominance of CD4+ T helper cell activity in both the blood and liver stages. However, more work defining CD8+ epitopes is warranted particularly since CD8+ T cells are primary effectors of pre-erythrocytic (sporozoite/liver) stage immunity. At the level of MHC restriction, we found low HLA diversity. Most defined epitopes are associated with alleles abundant in Caucasians populations, underscoring the need for the identification of epitopes recognized by a more diverse set of HLA molecules. Likewise for B cell epitopes, a striking experimental bias exists in the favour of definition of linear vs. discontinuous epitopes. We believe that defining Plasmodium-specific discontinuous epitopes will be an important area for future investigation, which will also benefit from high throughput definition of antibody antigen 3D structures.
Looking at the Plasmodium
species distribution for human pathogens, the vast majority of epitopes were described for P. falciparum
, followed distantly by P. vivax
, while in rodents as expected P. yoelii
and P berghei
constituted the majority of entries. Epitope identification studies may be desirable in several additional Plasmodium
species, and in those associated with non-human primates in particular to better correlate mechanisms of immunity and pathogenesis between animal models and human disease. In addition, further epitope identification in P. knowlesi
may be of significant interest, given the recent association of this species with human fatality (57
Despite the fairly broad distribution of epitopes among malarial proteins, we note that only a small fraction of the more than 5000 predicted ORFs for Plasmodium species have been associated with defined epitopes. It is likely that these results reflect experimental bias rather that an extreme form of immunodominance in responses, as it is well-known that Plasmodium specific responses are broad and multi-specific. Thus, genome-wide searches for correlates of immunity for vaccine development and sequence comparisons for identifying diagnostic candidates may be of significant interest to those in the malaria research community.
Assessing how many epitopes are associated with reactivity to different life cycle stages has implications for identifying target epitopes and/or antigens for use in vaccines. Epitopes have been reported from antigens expressed in all three life cycle stages of the plasmodial parasite (150 total unique proteins), consistent with the long recognized fact that different life stages can be targeted by immune responses. In terms of function of the recognized proteins, the preponderance of reported epitopes was derived from antigens that are expressed at the parasite surface, during the sporozoite stage and/or the asexual erythrocytic stage of the infection. This seems to be true regardless of effector cell (antibody or T cell), and highlights the need for epitope identification in a more diverse set of plasmodial antigens.
The distribution of the hosts from which the epitopes are derived is relevant for malaria vaccine and diagnostic development. Epitopes were most frequently defined using human hosts, followed by murine hosts. In humans to date, epitope data has been reported for populations from most, if not all, countries in which malaria has been defined as problematic and from subjects of all age groups [adults, children, infants and neonates]. However lacking from the human epitope data is a better definition of epitopes associated with different malarial disease states. Further investigation is highly desirable and strongly recommended.
Because fields within the IEDB have been specifically designed for the capture of patient histories, it should be possible in the future to use this information to probe for different patterns of epitope recognition. However, the current data for malaria is not yet comprehensive enough to allow for this analysis, even though interesting trends were noted, and might be confirmed as additional reports are published and included in the IEDB.
While identification of protective epitopes (those that when used as immunogen provide protection against infection/disease) was fairly broad in animal models, no protective epitopes have been defined for humans, However, epitopes recognized in the course of natural infection represent targets for inclusion into epitope-based vaccines. Likewise, analysis of epitopic responses associated with differential activities in in vitro assays, taken as surrogates of protection, will be of significant interest.
One of the most promising applications of the IEDB is for human data relating to clinical trials evaluating the immunogenicity, safety and protective efficacy of different antigens and vaccine formulations. In this application, the IEDB could thus assist the process of vaccine development and testing. The data currently available in the epitope literature is somewhat limited and therefore does not reflect the large number of vaccine trials conducted to date. However, in the last few years a resurgence of interest and activity in malaria research has brought together several different scientific groups, basic scientists, clinical investigators, health organizations and funding agencies. It is possible to speculate that in the future, more data would become available relating to the immunogenicity and efficacy of different vaccine candidates. The paradigm, database structure, curation and analysis strategies developed for the purpose of the present analysis could be easily applied to hosting and curation of detailed immunological data that could be queried at any level of granularity.
Ultimately, it will be interesting to repeat this analysis in 3–5 years to evaluate the growth of epitope data for Plasmodium species, to assess to what extent knowledge gaps have been addressed, and further, to access how such growth correlates with the growth of genomic data. Moreover, tools available on the IEDB webpage, such as ‘Homology Mapping’ and ‘Epitope Conservancy Analysis,’ could be employed for further analysis to assess such things as the potential impact of variants (polymorphism) on Plasmodium immunity and/or to perform cluster analysis to further refine epitope analysis.