Systematic identification of cancer-specific MHC-binding peptides with

Abstract

Immunotherapy can revolutionize anti-cancer therapy if specific targets are available. Immunogenic peptides encoded by cancer-specific genes (CSGs) may enable targeted immunotherapy, even of oligo-mutated cancers, which lack neo-antigens generated by protein-coding missense mutations. Here, we describe an algorithm and user-friendly software named RAVEN (Rich Analysis of Variable gene Expressions in Numerous tissues) that automatizes the systematic and fast identification of CSG-encoded peptides highly affine to Major Histocompatibility Complexes (MHC) starting from transcriptome data. We applied RAVEN to a dataset assembled from 2,678 simultaneously normalized gene expression microarrays comprising 50 tumor entities, with a focus on oligo-mutated pediatric cancers, and 71 normal tissue types. RAVEN performed a transcriptome-wide scan in each cancer entity for gender-specific CSGs, and 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 in cancer cell lines and in a comprehensive tissue-microarray. Subsequently, RAVEN identified likely immunogenic CSG-encoded peptides by predicting their affinity to MHCs and excluded sequence identity to abundantly expressed proteins by interrogating the UniProt protein-database. The predicted affinity of selected peptides was validated in T2-cell peptide-binding assays in which many showed binding-kinetics like a very immunogenic influenza control peptide. Collectively, we provide an exquisitely curated catalogue of cancer-specific and highly MHC-affine peptides across 50 cancer types, and a freely available software (https://github.com/JSGerke/RAVENsoftware) to easily apply our algorithm to any gene expression dataset. We anticipate that our peptide libraries and software constitute a rich resource to advance anti-cancer immunotherapy.

C1 [Baldauf, Michaela C.; Gerke, Julia S.; Rubio, Rebeca Alba; Dallmayer, Marlene; Musa, Julian; Knott, Maximilian M. L.; Sannino, Giuseppina; Marchetto, Aruna; Li, Jing; Ohmura, Shunya; Orth, Martin F.; Gruenewald, Thomas G. P.] Ludwig Maximilians Univ Munchen, Fac Med, Inst Pathol, Max Eder Res Grp Pediat Sarcoma Biol, Thalkirchner Str 36, D-80337 Munich, Germany.

[Kirschner, Andreas; Thiel, Uwe] TUM, Childrens Canc Res Ctr, Munich, Germany.

[Blaeschke, Franziska; Feuchtinger, Tobias] Ludwig Maximilians Univ Munchen, Dr von Haunersches Childrens Hosp, Dept Pediat, Munich, Germany.

[Effenberger, Manuel; Schober, Kilian; Busch, Dirk H.] TUM, Inst Med Microbiol Immunol & Hyg, Munich, Germany.

[Kanaseki, Takayuki; Sugita, Shintaro; Hasegawa, Tadashi] Sapporo Med Univ, Dept Pathol, Sapporo, Hokkaido, Japan.

[Kiran, Merve M.] Yildirim Beyazit Univ, Med Fac, Dept Pathol, Ankara, Turkey.

[Akpolat, Nurset; Akatli, Ayse N.] Inonu Univ, Turgut Ozal Med Ctr, Dept Pathol, Malatya, Turkey.

[Rosman, Fernando C.] Hosp Municipal Jesus, Dept Pathol, Rio De Janeiro, Brazil.

[Ozen, Ozlem] Baskent Univ Hosp, Med Fac, Dept Pathol, Ankara, Turkey.

[Sugimura, Haruhiko] Hamamatsu Sch Med, Dept Tumor Pathol, Hamamatsu, Shizuoka, Japan.

[Baumhoer, Daniel] Univ Hosp Basel, Bone Tumor Reference Ctr, Inst Pathol, Basel, Switzerland.

[Kirchner, Thomas; Gruenewald, Thomas G. P.] Ludwig Maximilians Univ Munchen, Fac Med, Inst Pathol, Munich, Germany.

[Kirchner, Thomas; Gruenewald, Thomas G. P.] German Canc Consortium DKTK, Partner Site Munich, Heidelberg, Germany.

[Kirchner, Thomas; Gruenewald, Thomas G. P.] German Canc Res Ctr, Heidelberg, Germany.