Proteogenomic Discovery of Neoantigens Facilitates Personalized Multi-antigen Targeted T cell Immunotherapy for Brain Tumors

Abstract

Neoantigen discovery in pediatric brain tumors is hampered by their low mutational burden and scant tissue availability. We developed a low-input proteogenomic approach combining tumor DNA/RNA sequencing and mass spectrometry proteomics to identify tumor-restricted (neoantigen) peptides arising from multiple genomic aberrations to generate a highly target-specific, autologous, personalized T cell immunotherapy. Our data indicate that novel splice junctions are the primary source of neoantigens in medulloblastoma, a common pediatric brain tumor. Proteogenomically identified tumor-specific peptides are immunogenic and generate MHC II-based T cell responses. Moreover, polyclonal and polyfunctional T cells specific for tumor-specific peptides effectively eliminated tumor cells in vitro. Targeting novel tumor-specific antigens obviates the issue of central immune tolerance while potentially providing a safety margin favoring combination with other immune-activating therapies. These findings demonstrate the proteogenomic discovery of immunogenic tumor-specific peptides and lay the groundwork for personalized targeted T cell therapies for children with brain tumors.

Neoantigens: promising targets for cancer therapy

“…333 For example, a proteogenomic method that integrates NGS and MS data supports the development of highly target-specific, autologous, personalized neoantigen immunotherapy, especially for tumors with low TMB. 479,481,482 The prediction of neoantigens is also constrained by genetic heterogeneity, particularly the diverse somatic mutations in distinct cancer types, in different individuals and even within tumor subclone cells. A major cause of genetic heterogeneity in cancer is genomic instability, which is dynamically altered in distinct tumors and different stages.…”

Boosting Antitumor Immunity with an Expanded Neoepitope Landscape

“…With the advent of sequencing and proteomics technologies combined with computational data analysis, significant leverage for antigen discovery has been achieved (184). For example, proteogenomics protocols have been applied for cancer neoantigen discovery, which combines genomics-based mutation or splicesite identification and mass spectrometry-based peptide identification (88,185,186). Proteogenomics complemented with algorithms for the prediction of HLA binders significantly expanded the repertoire of cancer antigens (187)(188)(189).…”

“…Indeed, hundreds of putative mutated splice-site-derived neoantigens were identified, with some of them shared between many unique tumor samples, albeit only one of these peptides was confirmed in proteomics analysis (85,87). However, a proteogenomic analysis of medulloblastoma samples showed that aberrant splice-site-derived neoantigens were the primary source of neoantigens in this cancer type, which were shown to harbor the capacity to provoke an HLA class II-mediated T-cell response (88).…”

BamQuery: a proteogenomic tool for the genome-wide exploration of the immunopeptidome

“…Second, we wondered whether mutated TAs would be as tumor-specific as expected. We analyzed 45 8-11 amino acid long mutated peptides (7 from gene fusions, 28 from aberrant splice junctions, and 10 from single nucleotide variations, SNV) reported as tumor-specific in medulloblastoma (no RNA expression in GTEx) 38 . BamQuery could attribute a genomic location to 39 of them and mapped 7/10 SNV peptides to their reported genes (Extended Data Fig.…”