Presentation of the Goodpasture autoantigen to CD4 T cells is influenced more by processing constraints than by HLA class II peptide binding preferences

Class II molecules are believed to influence immune responses by selectively binding antigen-derived peptides for recognition by T cells. In Goodpasture's (antiglomerular basement membrane) disease, autoimmunity to the NC1 domain of the alpha 3-chain of type IV collagen (alpha 3(IV)NC1) is strongly associated with HLA-DR15. We have examined the influence of the peptide binding preferences of DR15 molecules on the selection of alpha 3(TV)NC1-derived peptides displayed bound to DR15 molecules on the surface of alpha 3(TV)NC1-pulsed DR15-homozygous Epstein-Barr virus-transformed human B cells. The preferences of DR15 molecules were investigated using a panel of 24 overlapping peptides spanning the sequence of alpha 3(IV)NC1. The alpha 3(TV)NC1-derived peptides selected for display to T cells were determined by biochemical analysis as reported previously (Phelps, R., G.,, Turner, A. N.,, and Rees, A. J., (1996) J., Biol. Chem. 271, 18549-18553). Three nested sets of naturally presented alpha 3(TV)NC1 peptides were detectable bound to DR15 molecules. Peptides representative of each nested set bound to DR15 molecules, but almost two-thirds of the alpha 3(TV)NC1 peptides studied had as good or better DR15 affinity than those identified as naturally processed. Thus alpha 3(IV)NC1 presentation to T cells is determined more by "processing factors" than by the preferences of relatively indiscriminate DR15 molecules. The results have important implications for the use of class II peptide binding data to aid identification of potential T cell epitopes, especially for antigens which, like alpha 3(IV)NC1, contain many sequences able to bind class II molecules.