Immunoprecipitation methods impact the peptide repertoire in immunopeptidomics

ABSTRACT: T cell-based immunotherapies, which have become a promising treatment approach for cancer patients, rely on the identification of human leukocyte antigen (HLA)-presented peptides. Mass spectrometry-based immunopeptidomics is the state-of-the-art method for the identification of clinically relevant naturally presented HLA-restricted tumor-associated antigens. In the last years, different methods for the immunoprecipitation-based isolation of HLA-presented peptides have been developed and are used in the field. Here, we performed a comparison of a column-based with a high-throughput 96-well method by analyzing the immunopeptidome of cell lines as well as primary solid and hematological tumor samples. Whereas no differences in the total number of identified peptides were observed, the column-based method identified method-exclusive peptides that featured higher hydrophobicity and exhibited improved predicted immunogenicity. Adding an additional acetonitrile elution step to the 96-well method could partially reduce this hydrophilic shift. In total, we showed that immunopeptidomics data is affected by the immunoprecipitation method used for isolation, which might have a critical impact on the selection of target antigens and has to be considered when selecting clinically relevant targets for the development of T cell-based immunotherapies.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): B Cell, Primary Cell, Monocyte, Permanent Cell Line Cell, Epithelial Cell, Cell Culture, Kidney, Blood

DISEASE(S): Chronic Lymphocytic Leukemia,Renal Clear Cell Carcinoma

SUBMITTER: Marcel Wacker  

LAB HEAD: Juliane S. Walz

PROVIDER: PXD041804 | Pride | 2023-07-05

REPOSITORIES: Pride