PT  - JOURNAL ARTICLE
AU  - Sri H. Ramarathinam
AU  - Pouya Faridi
AU  - Angela Peng
AU  - Pacman Szeto
AU  - Nicholas C. Wong
AU  - Andreas Behren
AU  - Mark Shackleton
AU  - Anthony W. Purcell
TI  - A peptide-signal amplification strategy for the detection and validation of neoepitope presentation on cancer biopsies
AID  - 10.1101/2020.06.12.145276
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.06.12.145276
4099  - http://biorxiv.org/content/early/2020/06/12/2020.06.12.145276.short
4100  - http://biorxiv.org/content/early/2020/06/12/2020.06.12.145276.full
AB  - Targeting the right cancer-specific peptides presented by Human Leukocyte antigen (HLA) class I and II molecules on the tumor cell surface is a crucial step in cancer immunotherapy. Numerous approaches have been proposed to predict the presentation of potential neoepitopes that may be targeted through immune-based therapies. Often founded on patient specific somatic mutations, the routine validation of their actual appearance on the tumor cell surface is a significant barrier to realising personalized cancer immunotherapy. This can be attributed to the lack of robust and adaptable assays for antigen presentation that offer the required sensitivity to deal with the limited amounts of patient tumor tissue available. Rather than personalize individual assays we propose the use mass spectrometry to identify tumor neoepitopes from HLA-bound peptides directly isolated form the surface of tumor biopsies. We have developed a microscale HLA-peptide complex immunoprecipitation protocol combined with tandem mass tagging (TMT) to directly sequence HLA-bound peptides using mass spectrometry. Using this strategy, we identified HLA-bound peptides from as few as ~1000 cultured cells and from a small piece (~1 mg) of whole melanoma tumour tissue, encompassing epitopes derived from Melanoma-associated antigens and potential neoantigens.Competing Interest StatementThe authors have declared no competing interest.