Most importantly, inclusion of epitopes that are immuno-responsive
to different arms of the host immune machinery, such as CTL and Th epitope combinations can enable stronger and more efficient immune responses, similar to responses achieved with adjuvant therapies (e.g., [45, 48, 49, 103]). Thus, our study provides a unique strategy to identify suitable epitope candidates for multi-gene/multi-type vaccines that are both highly conserved across the global HIV-1 population and highly likely to co-occur together in the same viral genome in various Saracatinib mouse HIV-1 subtypes and thus can be simultaneously targeted by multi-epitope vaccines. Some of these conserved epitopes have been included in several recently tested vaccine candidates that showed promising results; however, none have included associated epitopes from all three genes. For example, segments of Gag, Pol and Nef were included in the recent LIPO-5 lipopeptide vaccine trial that Idasanutlin showed T-cell responses
in ~50% of vaccines , yet it lacked associated epitopes from Pol (Additional file 11). Further, because the included epitopes are already derived from the lists of epitopes with experimentally demonstrated immunogenicity in humans, (e.g., the list of “”best defined”" CTL epitopes by Frahm et al., 2007 ), many challenges associated with the accuracy of computational epitope prediction (e.g., [87, 105, 106]) can be avoided. Moreover, while sequence conservation does not assure that the epitope will be strongly immunogenic (e.g., [107, 108]), associated epitopes reported in this study also exhibit a high degree of nucleotide sequence conservation which is not readily identifiable the by other tools, such as Epitope
Conservancy Analysis Tool , making them suitable targets for other types of treatments such as RNA interference . Notably, a high degree of amino acid sequence conservation is not the only factor that influences identification of epitopes as promising candidates. For example, several epitopes included in the association rule mining, namely, PIPIHYCAPA (Ab, Env), WASRELERF (CTL, Gag) and RKAKIIRDY (CTL, Pol), were not involved in any of the 60626 associations that we discovered, showing that high conservation at the amino acid level does not automatically translate into involvement in association rules and that other factors are also at play.