Abstract A009: Benchmarking the foreign antigen space of human malignancies
Authors: Slagter Maarten , Fanchi Lorenzo , Buuren Marit M. van , Calis Jorg J A , Schouten Philip , Linn Sabine , Hoogstraat Marlous , Velds Arno , Veelken Hendrik , Kerkhoven Ron M. , Menzies Andrew , Alexandrov Ludmil B. , Stratton Michael , Wessels Lodewyk , Schumacher Ton N. 
Published: November 2016

Abstract
In a number of studies evaluating checkpoint blockade efficacy in cancer treatment, high mutational load of the tumor has been shown to correlate with clinical response, consistent with the notion that T-cell recognition of mutation derived (neo)-antigens plays a sizable role in immune based tumor eradication. Mutational load varies widely between and within malignancies, and is now frequently used as a proxy for the foreignness of cancers. However, in the absence of any well-defined reference points, it is difficult to understand which human tumors can be considered substantially foreign on the basis of the neo-antigens they carry.
Here we aim to benchmark the foreign antigen space of human cancers against a series of pathogen genomes for which T cell control has been documented. For this purpose, we developed a neo-antigen prediction pipeline that processes single nucleotide variants, indels and structural variants and filters candidate neo-peptides based on i). probability of successful proteasomal processing, ii). HLA-affinity, iii). RNA expression and iv). dissimilarity from self proteins. Having gathered a set of experimentally identified HIV-derived peptides, we determined the precision of our pipeline to be ∼40% for the HLA*A0201 allele of MHC-I, a substantially higher precision than achieved using prior methodologies.
Using this strategy, we aim to answer three classes of questions. First, how do the foreign antigen spaces of different tumors and tumor subtypes compare to the predicted neo-antigen load of human pathogens which are known to be sufficiently foreign to be controlled by T-cells? Second, is the foreignness of virus-induced cancers, such as EBV-positive lymphomas and HPV+ head and neck carcinomas and cervical cancer primarily determined by viral proteins or by DNA damage derived antigens? Third, what are the total neo-antigen yields and yield rates of different types of DNA damage? In this, we contrast variants by transcript effects (e.g. single nucleotide variants vs. indels), their predicted role in oncogenesis (i.e. driver vs. passenger variants) or their likelihood of having been generated by any of the mutational processes operative in the tumor in question. Results of these and other analyses will be presented.
Citation Format: Maarten Slagter, Lorenzo Fanchi, Marit M. van Buuren, Jorg J A Calis, Philip Schouten, Sabine Linn, Marlous Hoogstraat, Arno Velds, Hendrik Veelken, Ron M. Kerkhoven, Andrew Menzies, Ludmil B. Alexandrov, Michael Stratton, Lodewyk Wessels, Ton N. Schumacher. Benchmarking the foreign antigen space of human malignancies [abstract]. In: Proceedings of the Second CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; 2016 Sept 25-28; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(11 Suppl):Abstract nr A009.