A comprehensive analysis of constitutive naturally processed and presented HLA-C*04:01 (Cw4)-specific peptides

Tissue Antigens. 2014 Mar;83(3):174-9. doi: 10.1111/tan.12282. Epub 2014 Jan 7.


The human B lymphoblastoid cell line C1R is widely regarded as human leukocyte antigen-A (HLA-A)/HLA-B negative and is therefore frequently exploited as a recipient cell line to study HLA class I functions. However, the normal levels of HLA-C*04:01 often hamper the investigation of introduced HLA class I allomorphs, which is particularly evident in sensitive applications such as mass spectrometry. Here we describe the comprehensive analysis of endogenous HLA-C*04:01 ligands expressed on the surface of C1R cells to (i) define a large sequence dataset of HLA-C*04:01 ligands, to (ii) refine the HLA-C*04:01 peptide-binding motif and (iii) to provide a resource that allows discrimination between peptides bound to introduced HLA class I subtypes and to the endogenous HLA-C*04:01 molecules.

Keywords: C1R cells; HLA-B*35:03; HLA-C*04:01; HLA-Cw4; antigen presentation; immunopeptidome; mass spectrometry.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Antigen Presentation / immunology*
  • Databases, Protein
  • Epitopes / immunology
  • HLA-C Antigens / chemistry
  • HLA-C Antigens / genetics*
  • HLA-C Antigens / immunology*
  • Humans
  • Molecular Sequence Data
  • Peptides / chemistry
  • Peptides / immunology*


  • Epitopes
  • HLA-C Antigens
  • HLA-C*04 antigen
  • Peptides