Nonclassical antigen processing and the implications for autoimmunity and infection

Recent advances in immunology have given us evidence that antigen processing and presentation are not as simple as the mutually exclusive, MHC class I and MHC class II pathways presented in many textbooks. Antigen processing is responsible for producing self-epitopes, which is critical in the maintenance of tolerance and prevention of autoimmunity. Foreign antigens, from sources such as viruses, bacteria, and fungi, must also be processed and presented to the immune system so that appropriate defense and protection mechanisms can be employed. In the first part of this thesis, we explored the role of aminoglycosides in translational readthrough. These antibiotics, such as gentamicin, decrease the fidelity of translation, and allow for readthrough of stop codons by inserting random amino acids instead of terminating translation at a stop codon. This can lead to the production of novel epitopes from normally untranslated regions. Results from our recombinant vaccinia virus system show that gentamicin not only allows for the processing of cryptic epitopes, but a robust CD8 + T cell response in vitro and in vivo is elicited. Implications for autoimmunity are explored. In the latter two manuscripts, the role of the nonclassical, proteasome-dependent, MHC class II-restricted pathway is investigated in tissue culture and a mouse model. In Chapter 3 we utilized reagents specific for influenza epitopes that have been previously described to be processed by the classical or the endogenous, proteasome-dependent pathway. We provide evidence that the endogenous pathway is regulated in vitro by several features including cell type, length of time in culture (primary cells vs. transformed cell lines), live vs. UV-inactivated influenza, and expression of the class II transactivator. In Chapter 4, we extend these studies to show that in vivo, the utilization of the endogenous pathway is also regulated by the age of the host. Taken together, these studies demonstrate how changes in molecular processes such as antigen processing have broad downstream implications for the generation of T cell responses, and the delicate balance between providing robust immune responses for fighting infection and the prevention of autoimmunity