Combined presentation and immunogenicity analysis reveals a recurrent RAS.Q61K neoantigen in melanoma
Aviyah Peri, Erez Greenstein, Michal Alon, Joy A. Pai, Tamir Dingjan, Shlomit Reich-Zeliger, Eilon Barnea, Chaya Barbolin, Ronen Levy, Claudia Arnedo-Pac, Shelly Kalaora, Bareket Dassa, Ester Feldmesser, Ping Shang, Polina Greenberg, Yishai Levin, Gil Benedek, Mitchell P. Levesque, David J. Adams, Michal Lotem, James S. Wilmott, Richard A. Scolyer, Göran B. Jönsson, Arie Admon, Steven A. Rosenberg, Cyrille J. Cohen, Masha Y. Niv, Nuria Lopez-Bigas, Ansuman T. Satpathy, Nir Friedman, Yardena Samuels
Aviyah Peri, Erez Greenstein, Michal Alon, Joy A. Pai, Tamir Dingjan, Shlomit Reich-Zeliger, Eilon Barnea, Chaya Barbolin, Ronen Levy, Claudia Arnedo-Pac, Shelly Kalaora, Bareket Dassa, Ester Feldmesser, Ping Shang, Polina Greenberg, Yishai Levin, Gil Benedek, Mitchell P. Levesque, David J. Adams, Michal Lotem, James S. Wilmott, Richard A. Scolyer, Göran B. Jönsson, Arie Admon, Steven A. Rosenberg, Cyrille J. Cohen, Masha Y. Niv, Nuria Lopez-Bigas, Ansuman T. Satpathy, Nir Friedman, Yardena Samuels
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Research Article Genetics Oncology

Combined presentation and immunogenicity analysis reveals a recurrent RAS.Q61K neoantigen in melanoma

Abstract

Neoantigens are now recognized drivers of the antitumor immune response. Recurrent neoantigens, shared among groups of patients, have thus become increasingly coveted therapeutic targets. Here, we report on the data-driven identification of a robustly presented, immunogenic neoantigen that is derived from the combination of HLA-A*01:01 and RAS.Q61K. Analysis of large patient cohorts indicated that this combination applies to 3% of patients with melanoma. Using HLA peptidomics, we were able to demonstrate robust endogenous presentation of the neoantigen in 10 tumor samples. We detected specific reactivity to the mutated peptide within tumor-infiltrating lymphocytes (TILs) from 2 unrelated patients, thus confirming its natural immunogenicity. We further investigated the neoantigen-specific clones and their T cell receptors (TCRs) via a combination of TCR sequencing, TCR overexpression, functional assays, and single-cell transcriptomics. Our analysis revealed a diverse repertoire of neoantigen-specific clones with both intra- and interpatient TCR similarities. Moreover, 1 dominant clone proved to cross-react with the highly prevalent RAS.Q61R variant. Transcriptome analysis revealed a high association of TCR clones with specific T cell phenotypes in response to cognate melanoma, with neoantigen-specific cells showing an activated and dysfunctional phenotype. Identification of recurrent neoantigens and their reactive TCRs can promote “off-the-shelf” precision immunotherapies, alleviating limitations of personalized treatments.

Authors

Aviyah Peri, Erez Greenstein, Michal Alon, Joy A. Pai, Tamir Dingjan, Shlomit Reich-Zeliger, Eilon Barnea, Chaya Barbolin, Ronen Levy, Claudia Arnedo-Pac, Shelly Kalaora, Bareket Dassa, Ester Feldmesser, Ping Shang, Polina Greenberg, Yishai Levin, Gil Benedek, Mitchell P. Levesque, David J. Adams, Michal Lotem, James S. Wilmott, Richard A. Scolyer, Göran B. Jönsson, Arie Admon, Steven A. Rosenberg, Cyrille J. Cohen, Masha Y. Niv, Nuria Lopez-Bigas, Ansuman T. Satpathy, Nir Friedman, Yardena Samuels

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Figure 10

Contrasting tetramer-specific clones reveals transcriptional clonal segregation.

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Contrasting tetramer-specific clones reveals transcriptional clonal segr...
(A) UMAP of cells from tetramer+ populations colored by phenotype cluster. (B) Distribution of cells across clusters within each patient sample. Tet+, tetramer+. (C) UMAP of cells from each patient sample colored by tetramer-enriched clone identity. tetPos, tetramer+. (D) Heatmap depicting gene expression of select cluster markers and canonical T cell subset marker genes across the phenotypic clusters identified. (E) Gene expression module scoring of tetramer+ clusters with previously published CD8+ T cell gene sets (select signatures from ref. 49 and refs. 66–68). (F) Distribution of cells across phenotype clusters within each tetramer-enriched clone. (G) Comparison of T cell activation scores (from ref. 50) between each tetramer-enriched clone, other highly expanded clones in the bulk population, and all other unexpanded clones. The number of cells in each clone or group is indicated. (H) Gene signatures of each tetramer-enriched clone (for clones with >5 cells). (I) Spearman correlation of tetramer-enriched clones based on clone-specific gene signatures as defined in H.