Identification of T cell differentiation drivers towards exhaustion and anergy via multiplexed interventions

• Applicant: Professor Dr. Manfred Claassen, Ph.D.
• Subject Area: Immunology ; Bioinformatics and Theoretical Biology
• Term: since 2021
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 450981591

T cell exhaustion is an immune cell state associated with persistent viral infections as well as with impaired host immune defense in cancer affecting more than 2 billion people worldwide. Anergy is another distinct immune cell state also evoked by continuous antigen exposure, but, as opposed to chronic infections, in absence of inflammation. The causal molecular mechanisms leading to exhaustion and anergy remain elusive due to the difficulty to account for the complex and dynamic interplay of regulators of T cell differentiation in vivo.We aim at identifying novel causal transcriptional mechanisms - expanding on the few known candidates such as TOX - leading to T cell exhaustion and to this end, propose an integrated multiplexed, in vivo, single-cell intervention screen and causal inference approach. We study CD8+ T cell exhaustion in the context of acute and chronic lymphocytic choriomeningitis virus (LCMV) infection in mice, a well-established and recognized in vivo model system for persistent viral infections. We will perform a multiplexed CROP-seq intervention screen in conjunction with time series single cell RNA seq readout of antigen specific CD8+ T cells in the course of chronic infection. We propose deriving causal Markov models from the resulting data by comparative and integrative RNA velocity analysis. This approach will generate testable hypotheses on specific driver genes deciding on the fate of CD8+ T cells. Validation of fate determining potential of these genes will be performed in vivo by selective targeting in LCMV-specific CD8+ T cells. Validated mechanisms and driver genes in our in vivo model system will motivate rational interventions to beneficially interfere with T cell exhaustion in the context of human chronic infections or cancer.

• DFG Programme: Research Grants
• International Connection: Switzerland
• Cooperation Partner: Professorin Dr. Annette Oxenius