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Exploring affinity-dependent metabolic imprinting of anti-viral T cell responses

Primary Supervisor: Dr Heather Long, Institute of Immunology and Immunotherapy

Secondary supervisor: Dr Sarah Dimeloe

PhD project title: Exploring affinity-dependent metabolic imprinting of anti-viral T cell responses

University of Registration: University of Birmingham

Project outline:

T lymphocytes (T cells) are critical for anti-viral immunity, through their roles co-ordinating the immune response and directly killing virus-infected cells. They become activated when their T cell receptor (TCR) recognises viral peptides presented by major histocompatibility molecules (MHC) on antigen-presenting cells. Often, T cells with distinct, unique TCRs recognise the same viral peptide in complex with MHC, but with different affinity (strength of binding). Importantly, the strength of this interaction critically influences the T cell response elicited, with implications for both the type and scale of the primary T cell response to infection, and the differentiation and longevity of protective memory T cells. Precisely how TCR affinity programmes the T cell response is not fully understood, but warrants investigation, since this will inform the effective design of vaccines and adoptive T cell therapies.

Research over the last decade has revealed that T cell differentiation and function is fundamentally underpinned by changes in their metabolism that occur in response to TCR ligation. For example, activated T cells take up more glucose and amino acids and alter their metabolic pathway usage, which directly supports cellular proliferation, gene transcription and protein translation. Notably, recent studies interrogating genetically-manipulated TCRs identified that the strength of the TCR signal may control this metabolic reprogramming and thereby determine the resulting T cell phenotype. However, the role of TCR affinity in determining T cell metabolism and subsequent immune function in naturally generated virus-specific human T cells is unknown.

The student will interrogate this question, working across the labs of Dr Long and Dr Dimeloe, who have distinct and complementary expertise in anti-viral immunity and immunometabolism. This interdisciplinary approach is vital because such research is uniquely possible in a setting where defined T cell target peptides and reagents for single T cell analyses exist. The project will take advantage of Dr Long’s extensive experience in Epstein-Barr virus, where she has established such methodology, and may be extended to Sars-CoV-2, where Dr Long is currently defining T cell target peptides.

Firstly the student will explore the relationship between TCR binding affinity and T cell phenotype of EBV-specific T cells, employing EBV pMHC tetramers (optimised in Dr Long’s lab) in flow cytometry to identify peptide-specific T cells, and simultaneously interrogate their immune phenotype and functional capacities. In parallel, peptide-specific T cells will be purified and expanded in vitro to generate cell clones with unique TCRs, the sequences of which will be determined by DNA sequencing.

Next, the metabolic basis for TCR affinity-dependent T cell phenotype will be interrogated, using experimental approaches established in Dr Dimeloe’s lab. The student will assess whether antigen affinity correlates with mitochondrial mass and activity, as well as expression and function of key nutrient transporters in primary human T cells, by combining pMHC tetramer staining (as above) with fluorescent antibodies and metabolic probes for flow cytometry. Extracellular flux analysis and stable isotope-based metabolic tracing will be used to comprehensively assess the metabolic capacity and pathway usage of T cell clones with unique TCRs of different affinity. There will be an opportunity to visit Prof Christoph Hess’s laboratory in Basel to learn further specialised metabolic assays.

Finally, the student will explore the mechanistic basis for how TCR affinity controls T cell metabolic reprogramming, through analysis of key T cell signalling pathways known to instruct the metabolic phenotype and interrogation of unbiased transcriptomics datasets.

References:

  1. Long HM et al 2019. Front Immunol.  https://doi.org/10.3389/fimmu.2019.02193
  2. Munford and Dimeloe 2019. Front Mol Bio. https://doi.org/10.3389/fmolb.2019.00118

BBSRC Strategic Research Priority: Understanding the Rules of Life: Immunology

Techniques that will be undertaken during the project:

  • Flow cytometry
  • MHC tetramer analysis
  • T cell cloning
  • Metabolic extracellular flux analysis
  • Stable isotope-based metabolic tracing analysis

Contact: Dr Heather Long, University of Birmingham