Student Theses and Dissertations

Date of Award


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RU Laboratory

Munz Laboratory


MHC class II antigens, autophagy, virus replication


MHC class II molecules generally present peptides derived from exogenous antigens after endocytosis. However, biochemical studies have revealed that MHC class II ligands are frequently derived from intracellular proteins after endogenous processing. Endogenous MHC class II antigen presentation has been described for viral and model antigens and might represent an important mechanism to initiate CD4+ T cell responses to intracellular pathogens. We studied this unusual MHC class II presentation pathway using the Epstein- Barr virus nuclear antigen 1 (EBNA1) as a model antigen with relevance for human disease. We found that EBNA1 was degraded by lysosomal proteases and detected EBNA1 in double membrane structures by immuno-electron microscopy. Furthermore, inhibition of autophagy led to reduced stimulation of EBNA1-specific CD4+ T cells, suggesting that EBNA1 was delivered for MHC class II presentation by autophagy. This defines a new endogenous MHC class II processing pathway and EBNA1 is the first pathogen-derived antigen found to follow this pathway. To address the general relevance and the efficacy of this novel MHC class II pathway, we quantified autophagy in MHC class II-positive human cells and demonstrated constitutive autophagosome formation in epithelial, B and dendritic cells. The autophagosome marker Atg8/LC3 strongly overlapped with markers of MHC class II loading compartments (MIICs) by confocal and immuno-electron microscopy, suggesting that autophagosomes frequently fuse with MIICs. Furthermore, this pathway was of functional relevance, because targeting of influenza matrix protein 1 to autophagosomes via LC3 fusion led to strongly enhanced CD4+ T cell stimulation. This suggests that autophagy constitutively and efficiently delivers cytosolic antigens for MHC class II presentation and can be harnessed for improved helper T cell stimulation. In addition to its role in antigen presentation, autophagy might be an innate immune mechanism to restrict virus replication. We found that autophagosomes strongly accumulated in influenza A virus-infected lung epithelial cells, most likely because they do not fuse with lysosomes anymore. Infected cells contained unusually large autophagosomes filled with amorphous protein or nucleic acid, possibly of viral origin. Inhibition of autophagy led to an increase in influenza virus replication, suggesting that autophagy might be a mechanism to restrict or delay virus replication.


A thesis presented to the faculty of The Rockefeller University in partial fulfillment of the requirements for the degree of Doctor of Philosophy.

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