Distorted Relation between mRNA Copy Number and Corresponding Major Histocompatibility Complex Ligand Density on the Cell Surface

Abstract

The major histocompatibility complex (MHC) presents peptides derived from degraded cellular proteins to Tcells and is thus crucial for triggering specific immune responses against viral infections or cancer. Up to now, there has been no evidence for a correlation between levels of mRNA (the "transcriptome") and the density of MHC-peptide complexes (the "MHC ligandome") on cells. Because such dependences are of intrinsic importance for the detailed understanding of translation efficiency and protein turnover and thus for systems biology in general and for tumor immunotherapy in practical application, we quantitatively analyzed the levels of mRNA and corresponding MHC ligand densities in samples of renal cell carcinomas and their autologous normal kidney tissues. Relative quantification was carried out by gene chip analysis and by stable isotope peptide labeling, respectively. In comparing more than 270 pairs of gene expression and corresponding peptide presentation ratios, we demonstrate that there is no clear correlation (r ‫؍‬ 0.32) between mRNA levels and corresponding MHC peptide levels in renal cell carcinoma. A significant number of peptides presented predominantly on tumor or normal tissue showed no or only minor changes in mRNA expression levels. In several cases, peptides could even be identified despite the virtual absence of the respective mRNA. Thus we conclude that a majority of epitopes from tumor-associated antigens will not be found in approaches based mainly on mRNA expression studies as mRNA expression reflects a distorted picture of the situation on the cell surface as visible for T-cells.

Compartmentalized MHC class I antigen processing enhances immunosurveillance by circumventing the law of mass action

“…This suggests that the relevant antigen-processing compartment translates multiple mRNAs into DRiPs whose peptides compete for class I binding. Although our findings are limited to VV-derived peptides, it is likely that they extend to peptides derived from cellular proteins, because the findings provide an explanation for CD8 + T cell recognition of peptides encoded by low abundance or unusual mRNAs, as well as for the poor correlation between the immunopeptidome and the transcriptome or proteome (14)(15)(16). Consistent with the proposal that immunoribosomes translate nascent RNA (4), Gu et al (17) recently reported that truncated RNA generated via RNAi are an efficient source of antigenic peptides.…”

Exploring the MHC-peptide matrix of central tolerance in the human thymus

“…Interpretation of MS/MS fragmentation spectra was carried out manually using MassLynx 4.0 software 47 . For manual peptide identification, sequence tag searches were done using Mascot 2.0 software (peptide and MS/MS tolerance, 0.2 Da; National Center for Biotechnology Information non-redundant (NCBInr) database updated monthly and restricted for search to human entries), and relevant hits were assessed manually and not by evaluation of the Mascot score.…”

Long-Term Immunity against Actual Poxviral HLA Ligands as Identified by Differential Stable Isotope Labeling

“…This strategy is based on a technique recently established in our laboratory (36) to compare the repertoires of HLA ligands of tumor and healthy tissue (37,38). We found 15 viral peptides, of which 12 were presented by HLA-A*0201 and 3 by HLA-B*0702.…”