In the absence of Ii, MHC class II molecules display a distinct set of self peptides

The influence of the invariant (Ii) chain on antigen presentation by MHC class II molecules is well established. This study addresses whether the absence of Ii leads merely to failure of presentation of certain peptides or to display of novel peptides from endogenous proteins, using transfectants expressing HLA-DR alone, DR + Ii, or DR + Ii + DM. Western blotting revealed that, in the absence of Ii and DM, DR molecules form complexes with multiple intracellular proteins, furthermore, HPLC traces of peptides acid extracted from DR molecules expressed with or without Ii were markedly different. T cells were then used as “probes” of peptide occupancy of DR1. Most anti-DR1 alloreactive T cell clones raised against DR1 PBMC did not recognise DR1 in the absence of Ii and DM. Responses of clones that recognized the DR1⁺Ii^?DM^? transfectants were augmented by co-expression of Ii and DM. In contrast, anti-DR1 clones generated against the DR1⁺Ii^?DM^? transfectants failed to respond to human DR1-B-LCL. Responses to the DR1⁺Ii^?DM^? transfectants were abolished by co-expression of Ii and DM in the transfected cell line, excluding simple lineage-specific allorecognition. These results suggest that, in the absence of Ii, class II molecules display a distinct set of peptides, generated as a result of interactions with proteins early in the biosynthetic pathway. If circumstances arise in vivo when the ratio of Ii to MHC class II is reduced, this may lead to the display of “illegitimate” self peptides, and the consequent interruption of self tolerance.