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

Abstract

The entirety of human leukocyte antigen (HLA)-presented peptides is referred to as the HLA ligandome of a cell or tissue, in tumours often termed immunopeptidome. Mapping the tumour immunopeptidome by mass spectrometry (MS) comprehensively views the pathophysiologically relevant antigenic signature of human malignancies. MS is an unbiased approach stringently filtering the candidates to be tested as opposed to epitope prediction algorithms. In the setting of peptide-specific immunotherapies, MS-based strategies significantly diminish the risk of lacking clinical benefit, as they yield highly enriched amounts of truly presented peptides. Early immunopeptidomic efforts were severely limited by technical sensitivity and manual spectra interpretation. The technological progress with development of orbitrap mass analysers and enhanced chromatographic performance led to vast improvements in mass accuracy, sensitivity, resolution, and speed. Concomitantly, bioinformatic tools were developed to process MS data, integrate sequencing results, and deconvolute multi-allelic datasets. This enabled the immense advancement of tumour immunopeptidomics. Studying the HLA-presented peptide repertoire bears high potential for both answering basic scientific questions and translational application. Mapping the tumour HLA ligandome has started to significantly contribute to target identification for the design of peptide-specific cancer immunotherapies in clinical trials and compassionate need treatments. In contrast to prediction algorithms, rare HLA allotypes and HLA class II can be adequately addressed when choosing MS-guided target identification platforms. Herein, we review the identification of tumour HLA ligands focusing on sources, methods, bioinformatic data analysis, translational application, and provide an outlook on future developments.

New tools for MHC research from machine learning and predictive algorithms to the tumour immunopeptidome

“…Two recent papers have focused specifically on this renaissance of defining peptide presentation in complex antigenic environments by MHC elution and then mass spectrometry: the notion of defining an 'immunopeptidome'. 9,10 This has recently become a key resource for tumour immunology and the definition of targeted tumour antigens. A recent review article highlighted the progress made in the sphere of melanoma immunology through partnering direct analysis of tumour-infiltrating lymphocytes, MHC predictive algorithms and the MHCbound, mass-spectrometry-determined melanoma immunopeptidome.…”

“…9 From the University of Tubingen, arguably the birthplace of immunopeptidome research, now comes a major, comprehensive review on state-ofthe-art use of mass spectrometry to characterize tumour immunopeptidomes. 10 For anyone seeking new insights into tumour immunology and new prospects for immunotherapy, Freudenmann et al offer a masterclass that crosses different tumour types, peptide elutions and bioinformatics strategies.…”

“…Two recent papers have focused specifically on this renaissance of defining peptide presentation in complex antigenic environments by MHC elution and then mass spectrometry: the notion of defining an ‘immunopeptidome’ . This has recently become a key resource for tumour immunology and the definition of targeted tumour antigens.…”

“…A recent review article highlighted the progress made in the sphere of melanoma immunology through partnering direct analysis of tumour‐infiltrating lymphocytes, MHC predictive algorithms and the MHC‐bound, mass‐spectrometry‐determined melanoma immunopeptidome . From the University of Tubingen, arguably the birthplace of immunopeptidome research, now comes a major, comprehensive review on state‐of‐the‐art use of mass spectrometry to characterize tumour immunopeptidomes . For anyone seeking new insights into tumour immunology and new prospects for immunotherapy, Freudenmann et al .…”

Proteogenomic discovery of cancer antigens: Neoantigens and beyond

“…Technological advances in the last decade such as the development of orbitrap MS have improved its sensitivity and have significantly contributed to the effectiveness of the analysis. In order to isolate a set of peptides bound to HLA molecules, classical proteomics employs immunoprecipitation (IP) using antibodies which capture pHLA complexes from the cell lysate of either cell lines or primary tissues . Both HLA class I and II antibodies are available for IP, and there are two approaches, one of which uses pan‐class I antibodies while the other uses specific antibodies for each HLA type.…”