Elucidating the lineage dynamics of optimal human CD8 T cell responses to SARS-CoV-2 and how CD8 T cell homeostasis is altered in Long COVID

Project Summary/Abstract CD8 T cells are critical to the adaptive immune response to viral pathogens. When neutralizing antibodies are insufficient to prevent viral infection outright, virus-specific memory CD8 T cells can rapidly kill infected cells and limit the severity of infection. This has recently been identified as a potentially key mechanism by which COVID- 19 disease severity is reduced in vaccinated individuals. Memory CD8 T cells are functionally heterogeneous within and between individuals, with some cells more capable of effectively responding during viral infection. In the worst cases, dysfunctional CD8 T cell responses or ongoing responses to chronic viral infections could cause persistent and debilitating symptoms, as may be the case in Long COVID. Our understanding of the dynamics of human CD8 T cell differentiation remains incomplete, including why individuals generate functionally different responses to an identical antigen. Developing effective vaccines will require an understanding of shared molecular programs that can lead to potent effector responses across a range of individual immune landscapes and CD8 T cell identities. Two key gaps in knowledge impair our ability to fully leverage the potential of T cells in vaccines. First, little is known about the lineages that produce functionally distinct T cells in humans and what factors promote different lineages. Second, it is unclear which CD8 T cell states retain the greatest capacity to mount a potent effector response to combat infection. Therefore, there is an urgent need to define human memory CD8 T cell differentiation trajectories, how they impact future responses to viral pathogens, and how they may be dysregulated in cases where symptoms fail to resolve, such as Long COVID. We will address this need by testing three working hypotheses: first, that T cell clones differentiate down lineages with distinct functional capacities; second, that epigenetic features leave some lineages poised to mount more potent responses; and third, that the immune landscape influences CD8 T cell differentiation and functionality, with multiple classes of immune dysregulation driving Long COVID pathology. In Aims 1-2, we will use custom HLA- I/peptide tetramers to sort rare Spike-specific CD8 T cells from 5 individuals at each of a longitudinal series of memory and acute responding time points. We will then perform two cutting-edge single-cell sequencing approaches that use T cell receptor and mitochondrial variant sequences to define T cell clones and track the differentiation of these clones over time while assessing cell states by mRNA expression, protein expression, and chromatin accessibility. Aim 3 will use a systems immunology approach in healthy vaccinees and Long COVID patients to identify features of the immune landscape that correlate with optimal, sub-optimal, and dysregulated CD8 T cell responses. Collectively, these studies will evaluate multiple possible causes of Long COVID and will define the CD8 T cell differentiation lineages that produce optimal responses, providing a blueprint for improved vaccines to reduce severe disease caused by SARS-CoV-2, Influenza, and other viruses.