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

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

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Department of Biochemistry and Molecular Biology, Monash University, Clayton, 3800, Victoria, Australia.


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.


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

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