PT  - JOURNAL ARTICLE
AU  - Michaela C. Baldauf
AU  - Julia S. Gerke
AU  - Andreas Kirschner
AU  - Franziska Blaeschke
AU  - Manuel Effenberger
AU  - Kilian Schober
AU  - Rebeca Alba Rubio
AU  - Takayuki Kanaseki
AU  - Merve M. Kiran
AU  - Marlene Dallmayer
AU  - Julian Musa
AU  - Nurset Akpolat
AU  - Ayse N. Akatli
AU  - Fernando C. Rosman
AU  - Özlem Özen
AU  - Shintaro Sugita
AU  - Tadashi Hasegawa
AU  - Haruhiko Sugimura
AU  - Daniel Baumhoer
AU  - Maximilian M. L. Knott
AU  - Giuseppina Sannino
AU  - Aruna Marchetto
AU  - Jing Li
AU  - Dirk H. Busch
AU  - Tobias Feuchtinger
AU  - Shunya Ohmura
AU  - Martin F. Orth
AU  - Uwe Thiel
AU  - Thomas Kirchner
AU  - Thomas G. P. Grünewald
TI  - Systematic identification of cancer-specific MHC-binding peptides with RAVEN
AID  - 10.1101/193276
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 193276
4099  - http://biorxiv.org/content/early/2017/09/24/193276.short
4100  - http://biorxiv.org/content/early/2017/09/24/193276.full
AB  - Immunotherapy can revolutionize anti-cancer therapy if specific targets are available. Recurrent somatic mutations in the exome can create highly specific neo-antigens. However, especially pediatric cancers are oligo-mutated and hardly exhibit recurrent neo-antigens. Yet, immunogenic peptides encoded by cancer-specific genes (CSGs), which are virtually not expressed in normal tissues, may enable a targeted immunotherapy of such cancers. Here, we describe an algorithm and provide a user-friendly software named RAVEN (Rich Analysis of Variable gene Expressions in Numerous tissues), which automatizes the systematic and fast identification of CSG-encoded peptides highly affine to Major Histocompatibility Complexes (MHC) starting from publicly available gene expression data. We applied RAVEN to a dataset assembled from more than 2,700 simultaneously normalized gene expression microarrays comprising 50 tumor entities, with a focus on sarcomas and pediatric cancers, and 71 normal tissue types. RAVEN performed a transcriptome-wide scan in each cancer entity for gender-specific CSGs. As a proof-of-concept we identified several established CSGs, but also many novel candidates potentially suitable for targeting multiple cancer types. The specific expression of the most promising CSGs was validated by qRT-PCR in cancer cell lines and by immunohistochemistry in a comprehensive tissue-microarray comprising 412 samples. Subsequently, RAVEN identified likely immunogenic peptides encoded by these CSGs by predicting the affinity to MHCs. Putative highly affine peptides were automatically crosschecked with the UniProt protein-database to exclude sequence identity with abundantly expressed proteins. The predicted affinity of selected peptides was validated in T2-cell peptide-binding assays in which many showed similar kinetics to a very immunogenic influenza control peptide.Collectively, we provide a comprehensive, exquisitely curated and validated catalogue of cancer-specific and highly MHC-affine peptides across 50 cancer entities. In addition, we developed an intuitive and freely available software to easily apply our algorithm to any gene expression dataset (https://github.com/JSGerke/RAVENsoftware). We anticipate that our peptide libraries and software constitute a rich resource to accelerate the development of novel immunotherapies.