TCR-agnostic identification of tumor-specific CD8 T cells

• Applicants: Professor Dr. Heiner Wedemeyer; Dr. Norman Woller
• Subject Area: Immunology ; Gastroenterology
• Term: since 2023
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 525807092

T cells play a critical role in limiting tumor progression. However, assessment of patient-specific T cell responses is still limited and is not feasible in clinical settings. We established a patented method to detect tumor-specific CD8 T cells. The overall aims of this proposal are to comprehensively validate these new markers in patients, to establish their role as novel CD8 T cell-associated biomarkers, to quickly detect polyclonal T cell responses against tumors and lastly, to investigate the clonal distribution and expression profiles of circulating and tissue-residing tumor-specific T cells. Specifically, we propose four distinct work packages (WPs) to provide insights into the regulation of HCC-specific T cell responses and their role in tumor immune control. By using next generation sequencing (NGS) of tumor tissue and HLA genotyping, we aim to identify neoantigens. These neoantigens will then be used for validation of the tumor-specific T cell expression profile (WP1). In WP2, we will take advantage of single cell mRNA sequencing of CD8 T cells derived from HCC patients to analyse the whole transcriptome. Furthermore, a cytokine array will be performed for pathogen- and tumor-specific T cells to clarify their disparity in response to activating stimuli. In WP3, we will comprehensively analyse the single cell sequencing data set. High dimensional data processing will be applied to investigate clonal compositions of circulating and tumor-residing CD8 T cells, analyse phenotypic variations of these compartmentalized T cells, and study clonotypic differences in terms of exhaustion and activation. This technique in combination with our patented method will be supportive to shed light on several aspects of T cell immunology in HCC as an important part of the immunological landscape. In the next work package (WP4.1), patients treated with checkpoint inhibitors will be monitored for tumor-specific CD8 T cells from baseline until the follow up. Their frequency over time and phenotypes will be evaluated and will be correlated with therapy responses determined by imaging methods. A high correlation between these two methods may provide a diagnostic tool that could be a complementary and cost-effective method to determine therapy responses. Additionally, we have a T cell data set acquired from samples of a unique long-term cohort of cirrhotic HCV patients after HCV cure. As several patients developed HCC during follow-up, we will be able to investigate the role of immunosurveillance based on CD8 T cells in the course of early HCC development (WP4.2). In brief, the profiling of T cells by spectral flow cytometry and single cell mRNA sequencing in combination with our method for TCR-agnostic identification of tumor-specific CD8 T cells of a broad variety of clinical samples will most likely provide in-depth insight into tumor immunity and may have diagnostic and even therapeutic potential.

• DFG Programme: Research Grants