Toward a Definition of Self: Proteomic Evaluation of the Class I Peptide Repertoire

Abstract

MHC class I molecules present host- and pathogen-derived peptides for immune surveillance. Much attention is given to the search for viral and tumor nonself peptide epitopes, yet the question remains, “What is self?” Analyses of Edman motifs and of small sets of individual peptides suggest that the class I self repertoire consists of thousands of different peptides. However, there exists no systematic characterization of this self-peptide backdrop, causing the definition of class I-presented self to remain largely hypothetical. To better understand the breadth and nature of self proteins sampled by class I HLA, we sequenced >200 endogenously loaded HLA-B*1801 peptides from a human B cell line. Peptide-source proteins, ranging from actin-related protein 6 to zinc finger protein 147, possessed an assortment of biological and molecular functions. Major categories included binding proteins, catalytic proteins, and proteins involved in cell metabolism, growth, and maintenance. Genetically, peptides encoded by all chromosomes were presented. Statistical comparison of proteins presented by class I vs the human proteome provides empiric evidence that the range of proteins sampled by class I is relatively unbiased, with the exception of RNA-binding proteins that are over-represented in the class I peptide repertoire. These data show that, in this cell line, class I-presented self peptides represent a comprehensive and balanced summary of the proteomic content of the cell. Importantly, virus- and tumor-induced changes in virtually any cellular compartment or to any chromosome can be expected to be presented by class I molecules for immune recognition.

Expanding the detectable HLA peptide repertoire using electron-transfer/higher-energy collision dissociation (EThcD)

“…Moreover, ∼40% of the source proteins are represented by at least two peptides bound to different HLA molecules. This broad representation of the cell's proteome by HLA class I is in agreement with the general belief that equitable sampling is necessary to comprehensively reflect the health status of the cell (31). However, although the major part of the proteome seemed suited for HLA sampling, the actual small number of peptides identified per source protein confirms that considerable selection of peptides takes place, related to proteolytic cleavage, efficiency of TAP and the binding affinity of the available HLA molecule (16,20).…”

Conformational Restraints and Flexibility of 14-Meric Peptides in Complex with HLA-B*3501

“…Peptide elution studies led to the identification of mainly 9-mer peptides bound to MHC class I (29,30), representing the major pool of 80 -90% of HLA class I-associated peptides (31) and T cell epitopes characterized so far (http://syfpeithi.bmi-heidelberg.com). However, longer peptides have to be considered as potential antigenic epitopes that can be recognized by T cells as shown in this study.…”

The nature and extent of contributions by defective ribosome products to the HLA peptidome

“…It was suggested before that translational machinery proteins contribute significantly to the MHC peptidome (52)(53)(54). However, of the translational machinery components, it was the ribosomal proteins that contributed more significantly to the high DRiPs factor HLA peptidome.…”

“…Viruses are large protein complexes (containing also DNA or RNA), and it was already noticed that DNA-and RNAbinding proteins are abundant contributors to the HLA peptidome (52)(53)(54). The overtaking of the cellular protein production machinery by the viruses very likely results in less than perfect synchrony in the production of the viral proteins needed for capsid assembly.…”