Selective isolation and identification of HLA-DR-associated naturally processed and presented epitope peptides

Activation of CD4 helper T-cells is mediated by the presentation of antigenic peptides in context of self-MHC class II molecules. So far, the rules after which antigen-presenting cells (APC) select a particular epitope within a given protein antigen have been not fully elucidated. Nevertheless, immunoaffinity purification of APC-derived MHC class II molecules and the subsequent elutions of their with associated naturally processed and presented peptide epitopes (NPPE) have helped tremendously in understanding the nature of this rather complex process. In the present study, a novel approach for identifying such NPPEs is introduced, which is based on the culture of APCs in a completely protein-free medium during the antigen presenting process. These APCs do still express a high level of MHC class II as determined by HLA-DR cell surface staining, but the repertoire of the associated NPPEs is drastically reduced when compared to peptides eluted from cells maintained under normal culture condition. Actually, reverse phase-high pressure liquid chromatography (RP-HPLC) revealed that the entire NPPE repertoire consisted of less than ten major peaks, which is more than a 100-fold reduction of background peptide peaks as seen in cells from serum-containing culture conditions. Feeding APCs with exogenous antigens further confirmed the advantage of this novel system. While exogenous antigen-derived peptide peaks in an NPPE-eluate from RP-HPLC are hardly to detect by conventional procedures, the very low background of serum- and protein-free cultured APCs immensely facilitated this process, providing an improved tool for the identification and characterization of NPPEs.