Antigen presentation profiling reveals recognition of lymphoma immunoglobulin neoantigens

Abstract

Cancer somatic mutations can generate neoantigens that distinguish malignant from normal cells 1–7. However, the personalized identification and validation of neoantigens remains a major challenge. Here we discover neoantigens in human mantle cell lymphomas using an integrated genomic and proteomic strategy that interrogates tumor antigen peptides presented by major histocompatibility complex (MHC) class I and class II molecules. We applied this approach to systematically characterize MHC ligands from 17 patients. Remarkably, all discovered neoantigenic peptides were exclusively derived from the lymphoma immunoglobulin (Ig) heavy or light chain variable regions. Although we identified MHC presentation of private polymorphic germline alleles, no mutated peptides were recovered from non-Ig somatically mutated genes. Somatic mutations within the immunoglobulin variable region were almost exclusively presented by MHC-II. We isolated circulating CD4 T-cells specific for immunoglobulin-derived neoantigens and found these cells could mediate killing of autologous lymphoma cells. These results demonstrate that an integrative approach combining MHC isolation, peptide identification and exome sequencing is an effective platform to uncover tumor neoantigens. Application of this strategy to human lymphoma implicates immunoglobulin neoantigens as targets for lymphoma immunotherapy.

A Targeted LC‐MS Strategy for Low‐Abundant HLA Class‐I‐Presented Peptide Detection Identifies Novel Human Papillomavirus T‐Cell Epitopes

“…Most studies to date used untargeted unbiased LC‐MS 2 detection, which detects large numbers of epitopes presented at higher abundance. Untargeted detection was used for identification of HLA binding motives,35 viral epitopes,36 and tumor mutation‐derived epitopes (neoepitopes) from cancer cell lines37, 38 or primary human tumor material 39, 40. However, this common workflow fails to identify low‐abundant peptides that might still be important for immunotherapy development.…”

T‐Cell Immunopeptidomes Reveal Cell Subtype Surface Markers Derived From Intracellular Proteins

“…In total, 15 MHC-class I ligandome data sets were generated. MHC class-I molecules were isolated and the associated peptides extracted as previously described [27,28]. In brief, cells were lysed for 20 min on ice in 20 mM Tris-HCl (pH 8), 150 mM NaCl, 1 % (w/v) CHAPS, 0.2 mM PMSF, 1x Halt™ Protease and Phosphatase Inhibitor Cocktail (Thermo Fisher Scientific, Rockford, USA) supplemented with complete protease inhibitor cocktail (Roche, Mannheim, Germany).…”

Specific Adoptive Cellular Immunotherapy in Allogeneic Stem Cell Transplantation

“…In addition, targeting highly tumor-specific neoantigens may further improve specificity [94][95][96][97]. Recently it was shown that potential clinically relevant neoantigens can be directly identified on patient tumor material by mass spectrometry and that these neoepitopes are indeed capable of inducing immune responses [97,98]. Such T-cell responses can therefore lead to strong antitumor immune responses in the absence of off-target reactivity, and ultimately result in better clinical outcome of treated patients.…”

“…Novel breakthrough technologies of genetic modification such as CRISPR/Cas9-mediated gene editing are highly suitable to modulate T cells towards a fine-tuned desired effect Specific Adoptive Cellular Immunotherapy in Allo-SCT Oncol Res Treat 2017;40:691-696 695 [93]. In addition, targeting highly tumor-specific neoantigens may further improve specificity [94][95][96][97]. Recently it was shown that potential clinically relevant neoantigens can be directly identified on patient tumor material by mass spectrometry and that these neoepitopes are indeed capable of inducing immune responses [97,98].…”