Identification and Characterization of HLA Class I-Restricted MYD88 L265P-Derived Peptides As Tumor-Specific Targets for Immunotherapy
Authors: Nelde Annika , Stickel Juliane S , Kowalewski Daniel Johannes , Wolz Oliver Olaf , Kanz Lothar , Langerak Anton W. , Muggen Alice F. , Bonzheim Irina , Fend Falko , Rammensee Hans-Georg , Stevanovic Stefan , Weber Alexander N.R. 
Published: October 2019

Abstract
Non-Hodgkin lymphomas (NHL) are frequent malignancies with considerable mortality. A recurrent somatic and oncogenic driver mutation in the Toll-like receptor adaptor gene MYD88, Leu265Pro (L265P) has been identified in up to 90% of certain NHL subtypes. Genetic alterations affecting a protein-coding region have the potential to generate mutation-derived peptides that are presented by HLA class I proteins and might be recognized by cytotoxic T cells. Because MYD88L265P is a widely occurring and tumor-specific mutation, we investigated the potential of MYD88L265P -containing peptides for CD8+ T cell mediated immunotherapy as a new therapeutic approach for MYD88L265P+ NHL.
Based on in silico prediction we identified potential HLA ligands encompassing the MYD88L265P mutation for several HLA class I allotypes. Functional characterization of the candidate HLA class I MYD88L265P-derived HLA class I ligands with regard to induction of T cell responses identified a set of immunogenic peptides for HLA-B*07 and -B*15. In one MYD88L265P-mutated NHL patient, memory T cell responses targeting three different MYD88L265P-derived HLA class I ligands were detected by IFN-γ ELISPOT. Efficient T cell priming was demonstrated in vitro using naïve T cells of healthy volunteers (HVs). In detail, three HLA-B*07 peptides (P1-3B*07) and one HLA-B*15-restricted peptide (P4B*15) were analyzed using artificial antigen-presenting cell-based (aAPC) in vitro priming experiments in three to six HVs, respectively. For all tested peptides proliferation of peptide-specific CD8+ T cells could be detected after in vitro priming. For the HLA-B*07-restricted ligands, peptide-specific CD8+ T cells could be induced in 6/6 (P1B*15), 1/3 (P2B*07) and 3/4 (P3B*07) HVs, respectively, with a maximum frequency of 14.1% peptide-specific CD8+ T cells. For the HLA-B*15-restricted ligand (P4B*15), peptide-specific CD8+ T cells could be induced in 2/3 HVs with a maximum frequency of 9.5% tetramer-positive CD8+ T cells. The functionality and specificity of peptide-specific CD8+ T cells after aAPC-based in vitro priming was validated by intracellular cytokine staining for IFN-γ and TNF-α as well as for the expression of the degranulation marker CD107a. In 3/3 HVs primed with P1B*07 (RPIPIKYKAM) as well as in 1/2 HVs primed with P4B*15 (HQKRPIPIKY), we detected specific and functional CD8+ T cell populations after stimulation with the mutated peptides, but not after stimulation with the corresponding wild type peptides (P1WT: RLIPIKYKAM, P4WT: HQKRLIPIKY). Furthermore, the peptide-specific cytotoxic activity of specific CD8+ T cells was demonstrated in a VITAL assay. The polyclonal P1B*07- and P4B*15-specific CD8+ T cells (0.12% and 0.76% peptide-specific T cells, respectively) lysed autologous peripheral blood mononuclear cells loaded with the mutated peptides, but not cells presenting the wild type peptides. P4B*15-specific CD8+ T cells showed 17.9% (±1.2%) MYD88L265P-peptide-specific cell killing at an E/T ratio of 1:1 compared to 2.6% (±1.2%) of non-specific cell lysis of unspecific effector cells against the same targets in three independent replicates, respectively. The specific lysis showed an E/T ratio-dependent manner as the specific lysis decreases with reducing E/T ratios. P1B*07-specific CD8+ T cells specifically killed 11.4% (±1.7%) of MYD88L265P loaded targets at an E/T ratio of 0.7:1 in comparison to 2.1% unspecific lysis of unspecific effector cells.
In this study, we identified and characterized MYD88L265P mutation-derived HLA class I ligands for T cell mediated immunotherapy. The strong immunogenicity of the HLA-B*07 and HLA-B*15-restricted mutation-derived peptides as well as the functionality and specificity of peptide-specific CD8+ T cells, demonstrated by cytotoxicity assays, underline the potential of the MYD88L265P mutation as tumor-specific target. These data highlight the potential of MYD88L265P mutation-specific immunotherapy as a novel broadly applicable and tumor-specific treatment approach for patients with MYD88L265P+ NHL.

Disclosures
Langerak: InVivoScribe: Patents & Royalties: Licensing of IP and Patent on BIOMED-2-based methods for PCR-based Clonality Diagnostics.; DAKO: Patents & Royalties: Licensing of IP and Patent on Split-Signal FISH. Royalties for Dept. of Immunology, Erasmus MC, Rotterdam, NL; Roche: Other: Lab services in the field of MRD diagnostics provided by Dept of Immunology, Erasmus MC (Rotterdam).