A large number of peptides of cytosolic origin associate to HLA-DR molecules in epithelial cells, showing a different pattern from conventional antigen presenting cells

Expression of MHC class II molecules by epithelial cells is found in the thymus but also in peripheral epithelia, in a variety of inflammatory conditions such as autoimmunity. Antigen presentation to T-cells by parenchymal cells which lack classical co-stimulatory molecules may be qualitatively different from that of professional APCs, but may be sufficient to maintain productive responses. To study antigen processing and presentation by epithelial cells, we have constructed an "epithelial APC" by transfecting HLA-DR4 (DRB1*0401), Ii and DM into rat insulinoma cells (RINm5F) and analysed the peptides bound to these DR molecules by mass spectrometry and sequencing. Self-proteins contributed the absolute majority of bound peptides in epithelial cells. These epithelial self peptides associated to HLA-DR4 were derived from cytoplasmic and internalized proteins in similar proportions. Most of the cytosolic proteins contributing to the DR4 peptide pool were enzymes. This pattern was very different from the peptide pool associated to DR4 in a DR4-expressing EBV-transformed cell line, where DR4-associated peptide were derived exclusively from exogenous (serum) or internalized self membrane proteins. These data sugest the that different pathways may be involved in the generation of class II peptides in non-professional APCs and have important implications in autoimmunity and T cell selection processes.