Concurrently expressed tumor neoantigens drive phenotypically distinct CD8 T cell responses

CD8 T cell responses against different tumor neoantigens occur simultaneously, yet little is known about the interplay of these responses or its impact on tumor control. Here, we characterized the CD8 T cell response against two co-expressed tumor neoantigens, SIINFEKL (SIIN) and SIYRYYGL (SIY), in a genetically engineered mouse model of lung adenocarcinoma. In this model, tumors are initiated in KrasLSLG12D;p53fl/fl (KP) mice by intratracheal installation of lentiviruses expressing Cre recombinase and the antigens as a fusion to luciferase (LucOS). In these KP LucOS mice, the CD8 T cell response peaks around 5 weeks post-tumor initiation and is dominated by expansion of cells specific to SIIN. SIY drives a much smaller T cell response, but it persists better over time. To further investigate phenotypic differences in the T cell responses against SIIN versus SIY, we subjected antigen-specific CD8 T cells from 5 week mice to paired single cell RNA and TCR sequencing using the 10X Genomics platform. SIIN- and SIY-specific CD8 T cells were sorted from the lungs of KP LucOS mice 5 weeks post-tumor initiation and subjected to paired RNA and TCR single cell RNA sequencing using the 10X Genomics platform.