Label-free Analysis of CD8+ T Cell Subset Proteomes Supports a Progressive Differentiation Model of Human-Virus-Specific T Cells

Pathogens trigger T cells to express distinct sets of effector proteins. To better understand the molecular mechanisms that drive functional specification, we used high-resolution mass spectrometry and label-free protein quantification to measure proteomic differences between the seven largest circulating human CD8 + T cell subsets. Hierarchical clustering of the proteomes placed naive and CD45RA-expressing effector-type T cells at the extremes of the spectrum, with central memory and other effector memory stages located in between. Prominent differences between the subsets included expression of specific granzymes, signaling proteins, and molecules involved in metabolic regulation and cell adhesion. Remarkably, whereas most of the proteomic relationships between the subsets occurred in linear variations, a small proportion of proteins was regulated only in discrete subsets. The data obtained from this proteome analysis correspond best to a progressive differentiation model in which specific stable traits are gradually acquired during development.