Proteomic atlas of T cell exhaustion defines proteostatic collapse

T cell exhaustion limits the success of cancer immunotherapies, yet the proteomic changes underlying this dysfunctional state remain poorly understood. We integrated transcriptomics, quantitative proteomics, turnover proteomics, and ubiquitin proteomics to construct a multi-omic atlas of T cell exhaustion. These studies identified pathways regulated through transcriptional and post-translational mechanisms, including degradative and nondegradative ubiquitin modifications, and uncovered widespread changes in proteostasis, metabolism, and DNA repair. Major shifts were revealed in the ubiquitin-proteasome system, as differential expression of E3 ubiquitin ligases correlates with immunotherapy outcomes. These findings position the collapse of proteostasis as a central, underappreciated feature of T cell exhaustion and reveal opportunities to restore T cell function. We demonstrate that overexpression of the E3 ligase RNF166 enhances T cell persistence in vitro and in vivo. This work defines proteome-turnover dynamics as a critical regulatory layer in progressive T cell dysfunction, with broad implications for advancing cancer immunotherapy through manipulation of E3 ligases.