Peptides displayed by antigen presenting cells in the thymus shape the T cell repertoire. We investigated the antigen processing machinery of the MHC class II presentation pathway and describe the differential expression of lysosomal proteases in compartments of the thymus and the peripheral lymphoid tissue. Overexpression of certain proteases found in the thymus and thymoma associated with myasthenia gravis is likely to affect tolerance induction and may promote the generation autoreactive CD4(+) T helper cells.
