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The most meaningful advancement in cancer treatment in recent years has been the emergence of immunotherapy. Checkpoint inhibitor blockade and adoptive T cell therapy have shown remarkable clinical effects in a wide range of tumour types. Despite these advances, many tumours do not respond to these treatments, which raises the need to further investigate how patients can benefit from immunotherapy. This effort can now take advantage of the recent technological progress in single-cell, high-throughput sequencing and computational efforts. In this review, we will discuss advances in different immunotherapies and the principles of cancer immunogenomics, with an emphasis on the detection of cancer neoantigens with human leucocyte antigen peptidomics, and how these principles can be further used for more efficient clinical output.

Introduction Studies in the past few years have suggested a key role for neo-antigens in cancer immunotherapy. Since neo-antigens are specifically expressed on the tumour, targeting them is not likely to induce tolerance or normal tissue toxicity, making them candidates for immunotherapy. Despite encouraging results in clinical trials using neo-antigens, peptide or RNA vaccines and adoptive cell transfer (ACT), only a handful of neo-antigens and their corresponding T-cells have been identified in patients. Material and methods In this study we are using a combination of a novel neo-antigen prediction pipeline and human leukocyte antigen (HLA) peptidomics to unbiasedly identify tumour associated antigens (TAAs) and neo-antigens in tumours derived from melanoma patients, characterise their interactions with their tumour infiltrating lymphocytes (TILs) and identifying their matched T-cell receptor (TCR) sequences. Results and discussions For the analysis we used few metastases derived from the same patients and observed high similarity in the metastases antigenic and T-cells repertoires. Using interferon gamma release measurements, tetramer staining and killing assays in vivo and in vitro we were able to show that neo-antigen-specific T-cell clones are more abundant, reactive and proliferative than T-cell clones against TAAs. These methods in combination with TCR sequencing of the neo-antigen clones and bulk TILs enabled us to identify the specificity and identity of 87.4% of the TIL population. Furthermore we were able to show that only few reactive neo-antigens are responsible for the complete killing of the autologous melanoma cells and the rejection of the tumour in vivo . Conclusion Suggesting that our combined pipeline can help to characterise patient antigen and T-cell repertoires and select antigens that would be beneficial for designing personalised immunotherapy.