Peptide Repertoire Changes Caused by Defects in Antigen Processing

By

Kristin Camfield Lind

Doctor of Philosophy in Molecular and Cell Biology

University of California, Berkeley

Professor Nilabh Shastri, Chair

MHC I molecules display peptides derived from intracellular proteins on the cell surface for recognition by CD8+ T cells. Presentation of these peptide:MHC I complexes (pMHC I) is important for elimination of viruses and transformed cells. In order to generate an effective CD8 T cell response, a high-quality set of pMHC I must be presented. However, the editing mechanisms that select these optimal pMHC I are not clear. In these studies, we used biochemical and immunological methods to examine the role of two ER-resident pMHC I editors, tapasin and ERAAP in shaping the pMHC I repertoire.

Analysis of tapasin-deficient mice revealed a qualitative loss as well as gain of some pMHC I. However, these changes did not overlap with the ERAAP-unedited pMHC I repertoire, indicating that tapasin edits peptides in a distinct way. Sequencing of peptides unique to tapasin-deficient cells revealed altered C-termini, suggesting that tapasin determines the peptide C-terminus while ERAAP shapes the peptide N-terminus.

We separately examined the allele-specific effects of ERAAP-deficiency on the H-2d pMHC I repertoire. In addition to Kd and Dd, these mice express Ld, an MHC I molecule which is particularly affected by loss of ERAAP. We found that ERAAP-deficiency has distinct effects on the peptide repertoire presented by each MHC I molecule. Analysis of the peptide sequences revealed unique peptides bound to all three MHC I, although long, structurally unique peptides were only found on Dd and Kd. Furthermore, using a T cell hybridoma specific for loss of ERAAP function, we identified and characterized an ERAAP-unedited peptide presented by Dd. Together, these findings highlight the importance of both tapasin and ERAAP in determining an optimal pMHC I repertoire.

ABSTRACT It is thought that American options always gain value as the time to the option's expiration date increases. Merton (1973) proved this result using simple arbitrage arguments for options on non-dividend paying stocks. However, market prices reveal that (i) an American put can increase in value as calendar time passes diminishing the options time to expiration and (ii) two puts which differ only in expiration cycle can "sell" for the same price (i.e. a zero differential time premium). This paper demonstrates that dividend payments can cause this seemingly anomalous time premium behavior for American put options.

An understanding of cognitive control is crucial for understanding high-level cognition and delineating the functional role of prefrontal cortex in supporting complex cognitive operations. In this paper, we approach the problem of cognitive control by examining the control needs of SHRUTI, a neurally plausible and cognitively motivated model of inference and decision-making. It is shown that processing via spreading activation has a number of limitations with respect to inference and decision-making, and specific forms of controlled processing is required to overcome these limitations. We propose a set of primitive, neurally plausible control mechanisms, including monitoring, filtering, selection, maintenance, organization, and manipulation, describe connectionist implementations of these primitive mechanisms, and demonstrate the use of several of these primitives in a complex control process. (c) 2004 Published by Elsevier B.V.

Cytotoxic T cells monitor MHC class I complexes on antigen presenting cells for the potential presence of any non-self peptides that could derive from viral infection or cancerous cells. Effective immune surveillance requires that MHC class I molecules display a peptide repertoire on the surface representing all cellular proteins. This ensures that foreign antigens from all sources are presented. How the peptide repertoire can be comprehensive despite the large differences in abundance and stability of individual proteins is not known.

The pioneer round of translation is the first round of translation that occurs on newly spliced mRNA. It is associated with nonsense-mediated decay of mRNAs, allowing cells to detect and eliminate the aberrant mRNAs containing premature stop codons. We showed here that the peptide presentation by MHC I molecules was strongly influenced by the pioneer round of translation. Inhibition of the pioneer round of translation by knockdown of CBP80, a nuclear cap-binding protein, reduced peptide presentation by MHC class I molecules on the cell surface without affecting global protein synthesis. On the other hand, introduction of premature stop codons changed mRNA stability without affecting peptide presentation by MHC I on the cell surface. In addition, intronless mRNAs bypassing the pioneer round of translation resulted in reduced MHC I presentation on the cell surface. Furthermore, knockdown of CBP80 led to the deficiency of the cytosolic peptides delivered by the transporter associated with antigen processing (TAP) for the MHC class I pathway. Together, these findings highlight the importance of the pioneer round of translation in deriving peptides to generate a comprehensive display of virtually all endogenous proteins for the immune surveillance