The proteomic landscape of resting and activated CD4+ T cells reveal insights into cell differentiation and function

CD4+ T cells (T helper cells) are cytokine-producing adaptive immune cells that activate or regulate the responses of various immune cells. The activation and functional status of CD4+ T cells is important for adequate responses to pathogen infections but has also been associated with auto-immune disorders and survival in several cancers. In the current study, we carried out a label-free high-resolution FTMS-based proteomic profiling of resting and T cell receptor-activated (72h) primary human CD4+ T cells from peripheral blood of healthy donors as well as SUP T1 cells. We identified 5,237 proteins, of which significant alterations in the levels of 1,119 proteins were observed between resting and activated CD4+ T cells. We confirmed several known T-cell activation-related processes such as IL-2 response, metabolic and signaling changes, cell cycle induction, differentiation into effector cells among others. Several stimulatory/inhibitory immune checkpoint markers were altered considerably between resting and activated CD4+ T cells. Network analysis identified several known regulatory hubs of CD4+ T cell activation, including IFNG, IRF1, FOXP3, AURKA, and novel hubs such as RIOK2. Comparison of primary CD4+ T cell proteomic profiles with human lymphoblastic cell lines revealed a substantial overlap, while comparison with mouse CD+ T cell data suggested interspecies proteomic differences.