Biochemical and functional characterization of mutant KRAS epitopes validates this oncoprotein for immunological targeting

Adham S Bear,Khatuna Gabunia,Sarah Mccuaig,Robert H Vonderheide,Lee P Richman,Miren L Baroja,Christina Costeas,Michael J Ford,Joseph Cesare,Avery D Posey,Benjamin A Garcia,Anze Smole,Tatiana Blanchard,Daniel J Powell,Chong Xu,Beatriz M Carreno,Mark H O’Hara,Gerald P Linette,John Scholler

doi:10.1038/s41467-021-24562-2

Abstract

Activating RAS missense mutations are among the most prevalent genomic alterations observed in human cancers and drive oncogenesis in the three most lethal tumor types. Emerging evidence suggests mutant KRAS (mKRAS) may be targeted immunologically, but mKRAS epitopes remain poorly defined. Here we employ a multi-omics approach to characterize HLA class I-restricted mKRAS epitopes. We provide proteomic evidence of mKRAS epitope processing and presentation by high prevalence HLA class I alleles. Select epitopes are immunogenic enabling mKRAS-specific TCRαβ isolation. TCR transfer to primary CD8+ T cells confers cytotoxicity against mKRAS tumor cell lines independent of histologic origin, and the kinetics of lytic activity correlates with mKRAS peptide-HLA class I complex abundance. Adoptive transfer of mKRAS-TCR engineered CD8+ T cells leads to tumor eradication in a xenograft model of metastatic lung cancer. This study validates mKRAS peptides as bona fide epitopes facilitating the development of immune therapies targeting this oncoprotein.

Highlights

Activating RAS missense mutations are among the most prevalent genomic alterations observed in human cancers and drive oncogenesis in the three most lethal tumor types
We utilized the neoantigen prediction tool antigen.garnish[24] to perform a comprehensive identification of candidate HLA class I allele-restricted mutant KRAS (mKRAS) G12 epitopes with recurrent amino acid substitutions (G12C, G12D, G12R, G12V) embedded within the 24 amino acid sequence derived from the WT KRAS protein
Epitopes derived from these 24-mer amino acid sequences were evaluated for predicted binding to HLA class I alleles to nominate HLA-A, HLA-B, and HLA-C nonamer (9-mer) and/or decamer (10-mer) mKRAS peptides (Supplementary Data 1, candidates

Summary

Introduction

Activating RAS missense mutations are among the most prevalent genomic alterations observed in human cancers and drive oncogenesis in the three most lethal tumor types. T cells can be isolated from the peripheral blood or tumor tissue of antigen-exposed cancer patients[10], induced and expanded from the peripheral blood of cancer patients following neoantigen vaccination[11], and generated in vitro utilizing the naive T-cell receptor (TCR) repertoire of healthy donors[12]. These observations have garnered interest in the development of neoantigentargeted cancer vaccines and adoptive T cell therapies

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