Carcinogenesis of renal cell carcinoma reflected in HLA ligands: A novel approach for synergistic peptide vaccination design

Abstract

Despite recent advances in immunotherapy of renal cell carcinoma (RCC), peptide vaccination strategies still lack an approach for personalized peptide vaccination that takes intra-and inter-tumoral heterogeneity and biological characteristics into account. In this study, we use an immunoprecipitation and mass spectrometry-based approach supplemented by network analysis of HLA ligands to target this goal. By analyzing HLA-presented peptides for HLA class I and II of 11 malignant and 6 non-malignant kidney tissue samples, more than 2,700 peptides and 1,600 corresponding source proteins were identified.

Mapping the tumour human leukocyte antigen (HLA) ligandome by mass spectrometry

“…Nevertheless, the isolation of high amounts of both HLA class I-and II-associated peptides from so far all investigated tumour entities does also plead for unimpaired HLA expression on human tumours. [2][3][4]9,10,13,14 Fractionated HLA class I IP of cell populations from enzymatically dissociated EOC with high peptide yields from EpCAM + CD45 À tumour cells further underscores this statement. 1 So far, in-depth investigations of the non-mutated immunopeptidome presented on native clinical samples have been published for AML, 9 CLL, 14 MM, 10 mantle cell lymphoma (MCL), 13 EOC, 1 glioblastoma (GBM), 2 and metastatic malignant melanoma (MMM).…”

“…In heterogeneous bulk tumour tissue, stromal cells contribute considerably to the immunopeptidome. Nevertheless, the isolation of high amounts of both HLA class I‐ and II‐associated peptides from so far all investigated tumour entities does also plead for unimpaired HLA expression on human tumours . Fractionated HLA class I IP of cell populations from enzymatically dissociated EOC with high peptide yields from EpCAM + CD45 − tumour cells further underscores this statement …”

“…HLA ligands have often been isolated from bulk tumour tissue . A more sophisticated approach has been proposed by Schuster et al .…”

“…Assisted by (open source) online tools or software such as GeneMANIA and Cytoscape, these are allocated to biological processes, molecular functions or interaction networks. Pathways involved in tumourigenesis or metastasis formation, which are highly enriched in malignant samples, serve as basis to select antigens, thus permitting almost tumour‐exclusive HLA presentation patterns . When using databases, clustering or annotation tools, it is essential to know the experimental origin of the data input, how up‐to‐date it is, and which curation procedures it underwent.…”

“…Primary human tumour samples HLA ligands have often been isolated from bulk tumour tissue. [1][2][3][4][5][6][7][8] A more sophisticated approach has been proposed by Schuster et al; enzymatic dissociation with collagenase and subsequent sorting of cell populations allows for fractional HLA ligandome profiling with verification of (target) antigens to be presented on cancer cells. 1 Immunopeptidomes of most haematological malignancies can be directly analysed from cell suspensions with optional enrichment of specific cell types.…”