Abstract 1891: Targeted mass spectrometry provides direct evidence of a human endogenous retrovirus type E (HERV-E) antigen presented on the surface of clear cell renal cell carcinoma cells
Authors: Barisic Stefan , Cherkasova Elena , Chen Yong , Pierre Stephanie , Childs Richard W. 
Published: July 2021

Abstract
Background: Previously, our group identified donor-derived T cells that mediated regression of metastatic clear cell renal cell carcinoma (ccRCC) in a patient who underwent an allogeneic hematopoietic stem cell transplant. A T cell clone isolated from this patient had direct cytotoxicity against ccRCC cells. Its target antigen was discovered to be encoded by a human endogenous retrovirus type E (named CT-RCC HERV-E) that had selective expression in ccRCC. Subsequent experiments showed this T cell clone recognized a cryptic 10-mer peptide called CT-RCC1 (ATFLGSLTWK), derived from a noncanonical open reading frame of the CT-RCC HERV-E and presented in the context of HLA-A11. This study aimed to establish a proteomic workflow using targeted parallel reaction monitoring (PRM) mass spectrometry (MS) for the direct identification of CT-RCC1 peptide in ccRCC HLA ligandomes and to use that platform to identify other CT-RCC HERV-E derived peptides presented in the context of more common HLA alleles such as HLA-A02.
Methods: In this study, four ccRCC cell lines were used: HLA-A11 positive/CT-RCC HERV-E positive, HLA-A11 negative/CT-RCC HERV-E positive, HLA-A11 positive/CT-RCC HERV-E negative and HLA-A11 negative/CT-RCC HERV-E negative. Additionally, we used the HLA-A11 positive/CT-RCC HERV-E positive cell line to create both beta 2-microglobulin and CT-RCC HERV-E CRISPR knockout lines. HLA-peptide complexes were immunopurified from cell lysates with anti-HLA Class I antibodies cross-linked to Protein A Sepharose beads. Peptides were separated from HLA molecules using Sep-Pak tC18 reverse phase separation columns and subjected to targeted parallel reaction monitoring (PRM) mass spectrometry (MS) analysis. Synthetic CT-RCC1 peptide was used to generate optimum PRM transitions, determine the best collision energy, and obtain the full fragment ion spectrum. Data analysis was done using the Skyline package.
Results: CT-RCC1 peptide was identified by targeted MS to be presented on the surface of HLA-A11 positive/CT-RCC HERV-E positive ccRCC cells but not in those same cells that had CT-RCC HERV-E or beta 2-microglobulin knocked out using CRISPR. Additionally, the CT-RCC1 peptide was not detected in cells which were naturally HLA-A11 negative, CT-RCC HERV-E negative, or both.
Conclusions: Targeted MS identified the HERV-E derived HLA-A11 restricted peptide CT-RCC1 to be expressed on the surface of ccRCC cells. This study defines a reproducible immunopeptidomic workflow using targeted MS for identifying other antigens derived from this HERV-E that may be presented in the context of common HLA alleles.
Acknowledgments: We acknowledge the NIH Intramural Research Program and Rancic O'Neill Renal Cell Cancer Research Fellowship Fund for supporting this project.
Citation Format: Stefan Barisic, Elena Cherkasova, Yong Chen, Stephanie Pierre, Richard W. Childs. Targeted mass spectrometry provides direct evidence of a human endogenous retrovirus type E (HERV-E) antigen presented on the surface of clear cell renal cell carcinoma cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1891.