Identification of Tumor Antigens in the HLA Peptidome of Patient-derived Xenograft Tumors in Mouse

Abstract

Personalized cancer immunotherapy targeting patient-specific cancer/testis antigens (CTA) and neoantigens may benefit from large-scale tumor human leukocyte antigen (HLA) peptidome (immunopeptidome) analysis, which aims to accurately identify antigens presented by tumor cells. While significant efforts have been invested in analyzing the HLA peptidomes of fresh tumors, it is often impossible to obtain sufficient volumes of tumor tissues for comprehensive HLA peptidome characterization. This work attempted to overcome some of these obstacles by using patient-derived xenograft tumors (PDX) in mice as the tissue sources for HLA peptidome analysis. PDX tumors provide a proxy for the expansion of the patient tumor by re-grafting them through several passages to immune-compromised mice. The HLA peptidomes of human biopsies were compared to those derived from PDX tumors. Larger HLA peptidomes were obtained from the significantly larger PDX tumors as compared to the patient biopsies. The HLA peptidomes of different PDX tumors derived from the same source tumor biopsy were very reproducible, even following subsequent passages to new naïve mice. A large number of CTA-derived HLA peptides were discovered, as well as several potential neoantigens/variant sequences. Taken together, the use of PDX tumors for HLA peptidome analysis serves as a highly expandable and stable source of reproducible and authentic peptidomes, opening up new opportunities for defining large HLA peptidomes when only small tumor biopsies are available. This approach provides a large source for tumor antigens identification, potentially useful for personalized immunotherapy.

MhcVizPipe: A Quality Control Software for Rapid Assessment of Small- to Large-Scale Immunopeptidome Datasets

“…To show the utility of this scoring approach, we selected a small immunopeptidomic dataset generated from eight representative tumor biopsies, recently published in the study by Rijensky et al. ( 55 ). This dataset is composed of biopsies of different cancer types, including head and neck, bile duct, lung, gastric, vascular, bladder, and pancreatic cancer.…”

“…Supplemental data in the study by Rijensky et al. ( 55 ) and Shraibman et al. ( 46 ) were used to calculate the QC scores.…”

Immunopeptidomics: Isolation of Mouse and Human MHC Class I- and II-Associated Peptides for Mass Spectrometry Analysis

“…are available (e.g., anti-HLA-A2 BB7.2) but were not tested here. Note that the W6/32 antibody is widely used and the most established antibody in the field; it enables the isolation of peptides presented by all HLA-ABC molecules in humans and was previously reported by expert laboratories to work from various biological sources such as fresh or frozen tissues 8 , 39 , peripheral blood mononuclear cells and bone marrow mononuclear cell 40 , biopsies 41 , xenografts 41 , 42 , autopsies 43 and plasma samples 44 , 45 .…”

“…The type of beads and the type of acidic elution buffer that are used to elute MHC-complexes from the beads can also be modified for troubleshooting 13 , 14 , 15 , 16 , 17 , 18 , 19 41 , xenograft 42 , 43 , autopsy 44 , and plasma 45 , 46 samples were also reported but remain challenging for nonexpert laboratories. Also, the total number of MHC-associated peptides expected is well documented for established cell lines (here, between ~2000 and ~10000 peptides depending on the cell line and antibody used), but the absolute amounts of naturally presented peptides that are efficiently pulled down by the technique remain debated.…”

Kita-Kyushu Lung Cancer Antigen-1 (KK-LC-1): A Promising Cancer Testis Antigen

“…CTA-based treatments include antibodies, vaccines and anti-CTA chimeric antigen receptor-modified T cells (CAR-Ts). Although several CTA-targeted therapies have achieved encouraging results in preclinical and early clinical trials, the anticancer effect of CTA-targeted immunotherapy is not ideal, so these immunotherapies have not yet been used in the clinic as first-line anticancer drugs [ 81 - 83 ].…”