For many years, the investigation of HLA class I-bound peptides was cumbersome and only resulted in the determination of HLA peptide motifs, which nevertheless proved – after translation into tools for epitope prediction – useful for the identification of viral T cell epitopes. In the meantime, we are able to characterize almost the entire HLA class I ligandome of cells or tissues by mass spectrometry revealing several thousand different MHC-presented peptides. The detailed characterization of cytomegalovirus-specific peptides has so far been hampered by the efficient down-regulation of MHC I molecules from the surface of infected cells.
Fig. 1: Work flow of project Z01 and interaction with other projects
Employment of HCMV deletion mutants, lacking certain immune evasion genes, now facilitates, for the first time, the application of HLA ligandomics in order to identify minute amounts of viral peptides, which are concealed by the vast majority of self-peptides of host origin. Enhanced detection of low abundant peptide species has been additionally improved by technological progress such as the development of orbitrap mass analyzers and enhanced chromatographic performance which translates into increased mass accuracy, sensitivity, and resolution. We can now determine changes in the self-ligandome in response to infection, drug treatment, or transformation. By characterizing the immunopeptidome we will be able to address questions about immunodominance, the relevance of early and late antigens as well as the hierarchy between T cell epitopes in one distinct donor. In addition, a comparison between in silico epitope prediction and real peptide presentation will be enabled.
Our goal is a complete map of the T cell response to HCMV infection including all commonly occurring HLA restrictions of HLA class I and class II. The respective peptide epitopes would not only serve as useful diagnostic tools but also be available for immunotherapeutic interventions. Our GMP production unit permits the production of clinical grade peptides for application in patients. This will promote the translation of the identified CMV immunopeptidomes into novel clinical applications.
Fig. 2: HCMV-derived peptides are presented by a wide range of HLA allotypes