Features of TAP-independent MHC class I ligands revealed by quantitative mass spectrometry

Eur J Immunol. 2008 Jun;38(6):1503-10. doi: 10.1002/eji.200838136.


TAP is responsible for transferring cytosolic peptides into the ER, where they can be loaded onto MHC molecules. Deletion of TAP results in a drastic reduction of MHC class I surface expression and alters the presented peptide pattern. This key molecule in antigen processing is tackled by several viruses and lost in some tumors, rendering the altered cells less vulnerable to T cell-based immune surveillance. Using the TAP-deficient cell line LCL721.174 and its TAP-expressing progenitor cell line LCL721.45, we identified and quantified more than 160 HLA ligands, 50 of which were presented TAP-independently. Peptides which were predominantly presented on the TAP-deficient LCL721.174 cell line had a decreased MHC binding affinity according to their SYFPEITHI and BIMAS score. About half of the identified TAP-independently presented peptides were not derived from signal sequences and may partly be generated by the proteasome. Furthermore, we have excluded the possibility that differences in HLA ligand presentation between LCL721.45 and LCL721.174 were due to varying expression of the source proteins or due to changes in the antigen loading complex. Features of peptides presented independently of TAP as well as proteasomal contribution to their generation provide an insight into basic immunological mechanisms.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • ATP Binding Cassette Transporter, Subfamily B, Member 2
  • ATP Binding Cassette Transporter, Subfamily B, Member 3
  • ATP-Binding Cassette Transporters / genetics
  • ATP-Binding Cassette Transporters / physiology*
  • Amino Acid Sequence
  • Antigen Presentation / drug effects
  • Antigen Presentation / immunology*
  • Cell Line
  • Cysteine Proteinase Inhibitors / pharmacology
  • Epitopes, T-Lymphocyte / analysis
  • Epitopes, T-Lymphocyte / immunology*
  • Epitopes, T-Lymphocyte / metabolism
  • Gene Deletion
  • Gene Expression / genetics
  • HLA Antigens / immunology
  • HLA Antigens / metabolism
  • HLA-A Antigens / immunology
  • HLA-A Antigens / metabolism
  • HLA-A2 Antigen
  • HLA-B Antigens / immunology
  • HLA-B Antigens / metabolism
  • Histocompatibility Antigens Class I / immunology*
  • Histocompatibility Antigens Class I / metabolism
  • Humans
  • Isotope Labeling
  • Peptide Fragments / analysis
  • Peptide Fragments / immunology
  • Peptide Fragments / metabolism
  • Proteasome Endopeptidase Complex / metabolism
  • Proteasome Inhibitors
  • Protein Binding / immunology
  • Protein Sorting Signals
  • Proteins / genetics
  • Proteins / metabolism
  • Tandem Mass Spectrometry


  • ATP Binding Cassette Transporter, Subfamily B, Member 2
  • ATP Binding Cassette Transporter, Subfamily B, Member 3
  • ATP-Binding Cassette Transporters
  • Cysteine Proteinase Inhibitors
  • Epitopes, T-Lymphocyte
  • HLA Antigens
  • HLA-A Antigens
  • HLA-A*02:01 antigen
  • HLA-A2 Antigen
  • HLA-B Antigens
  • Histocompatibility Antigens Class I
  • Peptide Fragments
  • Proteasome Inhibitors
  • Protein Sorting Signals
  • Proteins
  • TAP1 protein, human
  • TAP2 protein, human
  • Proteasome Endopeptidase Complex