A post-translational regulatory map of chronic antigen-driven human T cell dysfunction

T cells exposed to persistent antigen, either in the context of chronic viral infections or tumors, iteratively lose both self-renewal and cytotoxic capacity. Several transcriptional, epigenetic, and metabolic drivers of this process have been identified. However, the post-transcriptional regulatory mechanisms influencing the proteome of dysfunctional T cells are not well understood. Here we present a time-resolved cysteine reactivity landscape of human T cells during the development of chronic antigen-driven dysfunction. Persistent T cell receptor stimulation of human T cells following activation significantly remodeled the T cell proteome compared with cytokine-mediated expansion, including changes in canonical T cell exhaustion-associated proteins as well as proteins related to mitochondrial function, redox homeostasis, nucleotide metabolism, and cell cycle progression. Exhausted T cells displayed frequent reactivity changes in nucleotide-binding domains across several protein classes that were associated with progressive loss of mitochondrial ATP production and activation of nucleotide salvage. Our comprehensive proteomic resource thus reveals a unique set of post-transcriptional changes as part of an exhausted T cell program and lays the groundwork for novel cysteine-directed therapeutics to enhance cancer immunotherapy.