title: 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 T-cells 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.
authors.affiliation: Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany.
authors.forename: Andreas O
authors.initials: AO
authors.lastname: Weinzierl
authors.forename: Claudia
authors.initials: C
authors.lastname: Lemmel
authors.forename: Oliver
authors.initials: O
authors.lastname: Schoor
authors.forename: Margret
authors.initials: M
authors.lastname: Müller
authors.forename: Tobias
authors.initials: T
authors.lastname: Krüger
authors.forename: Dorothee
authors.initials: D
authors.lastname: Wernet
authors.forename: Jörg
authors.initials: J
authors.lastname: Hennenlotter
authors.forename: Arnulf
authors.initials: A
authors.lastname: Stenzl
authors.forename: Karin
authors.initials: K
authors.lastname: Klingel
authors.forename: Hans-Georg
authors.initials: HG
authors.lastname: Rammensee
authors.forename: Stefan
authors.initials: S
authors.lastname: Stevanovic
mesh_terms: D000595:Amino Acid Sequence; D017951:Antigen Presentation / Q000235:genetics; D018628:Gene Dosage; D006680:HLA Antigens / Q000737:chemistry; D006801:Humans; D007668:Kidney / Q000166:cytology* / Q000473:pathology*; D008024:Ligands; D008285:Major Histocompatibility Complex / Q000276:immunology*; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis; D010455:Peptides / Q000032:analysis / Q000737:chemistry; D012333:RNA, Messenger / Q000032:analysis / Q000235:genetics*
chemical_list: D006680:HLA Antigens; D008024:Ligands; D010455:Peptides; D012333:RNA, Messenger