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Expression of a self peptide derived from the alpha chain of MHC class II (I-Ed) in association with I-Ab was studied in the murine thymic microenvironment. Previous work using the mAb Y-Ae which specifically recognizes the E alpha-I-Ab complex had reported differential expression between the thymic medulla and the cortex of this peptide-MHC complex: MHC class II-positive stromal cells in the medulla were strongly positive, whereas this complex was barely detectable on cortical epithelial cells (cEpC) in situ. This difference in presentation of an abundant self peptide is intriguing, since the self protein from which this peptide is derived and the presenting MHC molecule are strongly expressed in both compartments. In this report we show by cell surface phenotype and functional assays that isolated cEpC express the E alpha-I-Ab complex at significant although lower levels than medullary dendritic cells (DC), when examined ex vivo. These results support the notion that cEpC and bone marrow-derived stromal cells present a similar set of self peptide-MHC complexes in situ. In addition, we detect intercellular transfer in situ of the E alpha determinant from radioresistant stromal cells to thymic DC, a mechanism which may enhance the efficacy of tolerance induction by spreading self antigens with the thymic microenvironment.

T cells recognize foreign protein antigens in the form of peptide fragments bound tightly to the outer aspect of molecules encoded by the major histocompatibility complex (MHC). Most of the amino-acid differences that distinguish MHC allelic variants line the peptide-binding cleft, and different allelic forms of MHC molecules bind distinct peptides. It has been demonstrated that peptide-binding to MHC class I involves anchor residues in certain positions and that antigenic peptides associated with MHC class I exhibit allele-specific structural motifs. We have previously reported an analysis of MHC class II-associated peptide sequences. Here we extend this analysis and show that certain amino-acid residues occur at particular positions in the sequence of peptides binding to a given MHC class II molecule. These sequence motifs require the amino terminus to be shifted one or two positions to obtain alignment; such shifts occur naturally for a single peptide sequence without qualitatively altering CD4 T-cell recognition.

Self peptides bound to self major histocompatibility complex (MHC) molecules have been implicated both in positive and in negative selection of T cells during intrathymic development. We report here that the novel MHC-restricted monoclonal antibody Y-Ae detects the MHC class II bound form of a major self peptide. Y-Ae binds approximately 12% of the relevant MHC class II molecules on self antigen presenting cells. The peptide detected by Y-Ae is one of several major peptides eluted from the MHC molecule. These data suggest that self peptides presented by self MHC class II molecules at densities sufficient to signal a CD4 T cell are of very limited complexity. Furthermore, as Y-Ae stains antigen presenting cells that mediate negative selection but not thymic cortical epithelial cells that drive positive selection, differential expression of self peptide:self MHC class II complexes may be a key feature of intrathymic selection.