TY - JOUR T1 - Targeting the tumor mutanome for personalized vaccination in a TMB low non-small cell lung cancer JF - Journal for ImmunoTherapy of Cancer JO - J Immunother Cancer DO - 10.1136/jitc-2021-003821 VL - 10 IS - 3 SP - e003821 AU - Katy McCann AU - Adrian von Witzleben AU - Jaya Thomas AU - Chuan Wang AU - Oliver Wood AU - Divya Singh AU - Konstantinos Boukas AU - Kaidre Bendjama AU - Nathalie Silvestre AU - Finn Cilius Nielsen AU - Gareth Thomas AU - Tilman Sanchez-Elsner AU - Jason Greenbaum AU - Stephen Schoenberger AU - Bjoern Peters AU - Pandurangan Vijayanand AU - Natalia Savelyeva AU - Christian Ottensmeier Y1 - 2022/03/01 UR - http://jitc.bmj.com/content/10/3/e003821.abstract N2 - Background Cancer is characterized by an accumulation of somatic mutations, of which a significant subset can generate cancer-specific neoepitopes that are recognized by autologous T cells. Such neoepitopes are emerging as important targets for cancer immunotherapy, including personalized cancer vaccination strategies.Methods We used whole-exome and RNA sequencing analysis to identify potential neoantigens for a patient with non-small cell lung cancer. Thereafter, we assessed the autologous T-cell reactivity to the candidate neoantigens using a long peptide approach in a cultured interferon gamma ELISpot and tracked the neoantigen-specific T-cells in the tumor by T-cell receptor (TCR) sequencing. In parallel, identified gene variants were incorporated into a Modified Vaccinia Ankara-based vaccine, which was evaluated in the human leucocyte antigen A*0201 transgenic mouse model (HHD).Results Sequencing revealed a tumor with a low mutational burden: 2219 sequence variants were identified from the primary tumor, of which 23 were expressed in the transcriptome, involving 18 gene products. We could demonstrate spontaneous T-cell responses to 5/18 (28%) mutated gene variants, and further analysis of the TCR repertoire of neoantigen-specific CD4+ and CD8+ T cells revealed TCR clonotypes that were expanded in both blood and tumor tissue. Following vaccination of HHD mice, de novo T-cell responses were generated to 4/18 (22%) mutated gene variants; T cells reactive against two variants were also evident in the autologous setting. Subsequently, we determined the major histocompatibility complex restriction of the T-cell responses and used in silico prediction tools to determine the likely neoepitopes.Conclusions Our study demonstrates the feasibility of efficiently identifying tumor-specific neoantigens that can be targeted by vaccination in tumors with a low mutational burden, promising successful clinical exploitation, with trials currently underway.Data are available in a public, open access repository. All data relevant to the study are included in the article or uploaded as online supplemental information. Sequencing data have been deposited in the Gene Expression Omnibus under accession number GSE179879. ER -