Single-cell transcriptomics identifies key components in metabolic pathways of drug perturbed activated CD4+ T cells
CD4+ T cells play a critical role in the development of autoimmune diseases. During CD4+ T cell activation, remodelling of metabolic pathways is required for the cells to exert their effector functions. The importance of these pathways is highlighted by the successful therapies for immune diseases that target metabolic pathways. Although key metabolic processes have been recognized to affect T cell activation and lineage development, how metabolic interventions can skew the outcome of T cells activation and differentiation remain largely unknown. I first introduce the experiments which guided the selection of 19 compounds targeting various metabolic pathways with measurements on murine CD8+ T cells and both naïve and memory human CD4+ T cells. I proceed to describe drug effects on CD4+ T cell day 3 proliferation and gene expression by single cell transcriptional profiling at resting state, 16 hours and 3 days after stimulation with aCD3/aCD28. My observations reveal cell subpopulations present only at certain activation time point and demonstrate drug effects altering gene expression and pathways within specific cell populations. Then, I characterise distinct pseudotime trajectories representing the progression from naïve to effector memory cells at each time point. With linear models, I identify the immune-related disease genes regulated by both drug effects and the effector status of cells. Leveraging RNA splicing information, I demonstrate that expression changes of genes targeted by compounds resulted in altered T cell lineage development. Furthermore, my analysis highlights important transcription factors and metabolic pathways regulated by the interactions between metabolic perturbation and effector function. The work in the dissertation presents a unique resource of metabolic perturbations in CD4+ T cells and provides insights into understanding the role of T cell metabolism in immune-mediated diseases.
CD4+ T cells, drug perturbation, single-cell, transcriptomics
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