NMD inhibition by 5-azacytidine augments presentation of immunogenic frameshift-derived neoepitopes

Jonas P Becker; Dominic Helm; Mandy Rettel; Frank Stein; Alejandro Hernandez-Sanchez; Katharina Urban; Johannes Gebert; Matthias Kloor; Gabriele Neu-Yilik; Magnus von Knebel Doeberitz; Matthias W Hentze; Andreas E Kulozik

doi:10.1016/j.isci.2021.102389

NMD inhibition by 5-azacytidine augments presentation of immunogenic frameshift-derived neoepitopes

iScience. 2021 Apr 1;24(4):102389. doi: 10.1016/j.isci.2021.102389. eCollection 2021 Apr 23.

Authors

Jonas P Becker^{1

2

3

4}, Dominic Helm⁵, Mandy Rettel², Frank Stein², Alejandro Hernandez-Sanchez^{1

2

6

7}, Katharina Urban^{1

2

6

7}, Johannes Gebert^{1

2

6

7}, Matthias Kloor^{1

2

6

7}, Gabriele Neu-Yilik^{1

2

3

4}, Magnus von Knebel Doeberitz^{1

2

6

7}, Matthias W Hentze^{1

2}, Andreas E Kulozik^{1

2

3

4}

Affiliations

¹ Molecular Medicine Partnership Unit (MMPU), Heidelberg University, 69120 Heidelberg, Germany.
² European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.
³ Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University, 69120 Heidelberg, Germany.
⁴ Hopp Children's Cancer Center, National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany.
⁵ Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
⁶ Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University, 69120 Heidelberg, Germany.
⁷ Collaboration Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.

Abstract

Frameshifted protein sequences elicit tumor-specific T cell-mediated immune responses in microsatellite-unstable (MSI) cancers if presented by HLA class I molecules. However, their expression and presentation are limited by nonsense-mediated RNA decay (NMD). We employed an unbiased immunopeptidomics workflow to analyze MSI HCT-116 cells and identified >10,000 HLA class I-presented peptides including five frameshift-derived InDel neoepitopes. Notably, pharmacological NMD inhibition with 5-azacytidine stabilizes frameshift-bearing transcripts and increases the HLA class I-mediated presentation of InDel neoepitopes. The frameshift mutation underlying one of the identified InDel neoepitopes is highly recurrent in MSI colorectal cancer cell lines and primary patient samples, and immunization with the corresponding neoepitope induces strong CD8⁺ T cell responses in an HLA-A∗02:01 transgenic mouse model. Our data show directly that pharmacological NMD inhibition augments HLA class I-mediated presentation of immunogenic frameshift-derived InDel neoepitopes thus highlighting the clinical potential of NMD inhibition in anti-cancer immunotherapy strategies.

Keywords: Biological Sciences; Cancer; Immunology.