The long term goals of this project are to understand how the antigen processing pathway generates peptide/MHC class I complexes (pMHC I) by cryptic translation. Numerous studies, from many different laboratories, have shown that naturally processed pMHC I on the surface of tumors, virally infected cells, transfected or even normal cells arise from regions of mRNAs that were not expected to be translated. The mechanism that allows cells to sample this cryptic source of antigenic precursors versus other conventional sources is obscure. In addition, to what extent cryptic peptides arise from normal mRNAs and contribute to the diverse pool of peptides presented by MHC class I molecules is unknown. Here we will test the hypotheses that (a) these unusual, cryptic peptides arise not only from mutated or exogenously introduced genes but also from normal genes and (b) their expression may be regulated under stress. Furthermore, we will test the hypothesis that (c) cryptic translation results from a novel set of ribosomes that initiate translation not at conventional AUG codons, but at cryptic non-AUG codons. We will characterize these ribosomes using primer extension inhibition (toeprinting) and by direct analyses of their t-RNAs, proteins and RNA constituents. We anticipate that an improved understanding of how cryptic pMHC I are generated will not only provide a means to tap into a novel sources of antigenic peptides and new approaches to vaccine design, but will also yield insights into protein translation and immune surveillance mechanisms.

Agency
National Institute of Health (NIH)
Institute
National Institute of Allergy and Infectious Diseases (NIAID)
Type
Research Project (R01)
Project #
5R01AI044864-08
Application #
7655549
Study Section
Cellular and Molecular Immunology - A Study Section (CMIA)
Program Officer
Rice, Jeffrey S
Project Start
2000-02-15
Project End
2011-07-31
Budget Start
2009-08-01
Budget End
2010-07-31
Support Year
8
Fiscal Year
2009
Total Cost
$367,049
Indirect Cost
Name
University of California Berkeley
Department
Biochemistry
Type
Schools of Arts and Sciences
DUNS #
124726725
City
Berkeley
State
CA
Country
United States
Zip Code
94704
Prasad, Sharanya; Starck, Shelley R; Shastri, Nilabh (2016) Presentation of Cryptic Peptides by MHC Class I Is Enhanced by Inflammatory Stimuli. J Immunol 197:2981-2991
Starck, Shelley R; Shastri, Nilabh (2016) Nowhere to hide: unconventional translation yields cryptic peptides for immune surveillance. Immunol Rev 272:8-16
Shastri, Nilabh; Nagarajan, Niranjana; Lind, Kristin C et al. (2014) Monitoring peptide processing for MHC class I molecules in the endoplasmic reticulum. Curr Opin Immunol 26:123-7
Nagarajan, Niranjana A; Shastri, Nilabh (2013) Immune surveillance for ERAAP dysfunction. Mol Immunol 55:120-2
Nagarajan, Niranjana A; Gonzalez, Federico; Shastri, Nilabh (2012) Nonclassical MHC class Ib-restricted cytotoxic T cells monitor antigen processing in the endoplasmic reticulum. Nat Immunol 13:579-86
Blanchard, Nicolas; Shastri, Nilabh (2010) Topological journey of parasite-derived antigens for presentation by MHC class I molecules. Trends Immunol 31:414-21
Blanchard, Nicolas; Shastri, Nilabh (2008) Coping with loss of perfection in the MHC class I peptide repertoire. Curr Opin Immunol 20:82-8
Schwab, Susan R; Shugart, Jessica A; Horng, Tiffany et al. (2004) Unanticipated antigens: translation initiation at CUG with leucine. PLoS Biol 2:e366