The Origin and Immune Recognition of Tumor-Specific Antigens

Simple Summary Cancer immunology is a rapidly evolving field. In this context, this review article has three objectives. First, to explain the genomic origin of tumor antigens and to emphasize that many of them are encoded by unconventional RNAs. Second, to discuss the inherent limitations of all strategies aimed at discovering tumor antigens, and to highlight the importance of using mass spectrometry validation for each antigen considered for clinical trials. Third, to explain that many tumor antigens are not spontaneously detected by the immune system, because they are not presented adequately by dendritic cells. Concepts presented in this article must be taken into account in the design of cancer immunotherapies and of cancer vaccines in particular. The dominant paradigm holds that spontaneous and therapeutically induced anti-tumor responses are mediated mainly by CD8 T cells and directed against tumor-specific antigens (TSAs). The presence of specific TSAs on cancer cells can only be proven by mass spectrometry analyses. Bioinformatic predictions and reverse immunology studies cannot provide this type of conclusive evidence. Most TSAs are coded by unmutated non-canonical transcripts that arise from cancer-specific epigenetic and splicing aberrations. When searching for TSAs, it is therefore important to perform mass spectrometry analyses that interrogate not only the canonical reading frame of annotated exome but all reading frames of the entire translatome. The majority of aberrantly expressed TSAs (aeTSAs) derive from unstable short-lived proteins that are good substrates for direct major histocompatibility complex (MHC) I presentation but poor substrates for cross-presentation. This is an important caveat, because cancer cells are poor antigen-presenting cells, and the immune system, therefore, depends on cross-presentation by dendritic cells (DCs) to detect the presence of TSAs. We, therefore, postulate that, in the untreated host, most aeTSAs are undetected by the immune system. We present evidence suggesting that vaccines inducing direct aeTSA presentation by DCs may represent an attractive strategy for cancer treatment.