Checkpoint-enriched T cells with retained effector-associated features are associated with disease activity in...

Systemic lupus erythematosus (SLE) is a chronic autoimmune disease characterized by sustained immune activation and fluctuating disease activity. Although exhaustion-associated markers are frequently detected on T cells from patients with SLE, the biological significance of these signatures remains poorly defined. Here, we performed high-dimensional phenotypic profiling of circulating CD8⁺ and CD4⁺ T cells from patients with inactive and active SLE using spectral flow cytometry, complemented by an in vitro model of sustained TCR stimulation. We identified distinct T cell subsets characterized by coordinated expression of multiple immune checkpoint receptors, including PD-1, LAG-3, TIM-3, TIGIT and CD39, together with the transcriptional regulator TOX. Notably, checkpoint-enriched populations were preferentially expanded in patients with active disease (aSLE). Despite the accumulation of inhibitory features, both CD8⁺ and CD4⁺ T cells retained effector-associated features, including cytokine production and cytotoxic mediator expression, suggesting that immune checkpoint expression in this context is not uniformly associated with the complete loss of effector-associated features characteristic of canonical T cell exhaustion. Trajectory inference of ex vivo datasets, together with the in vitro model, suggested an association between sustained activation and increasing immune checkpoint receptor expression while maintaining the expression of effector-associated molecules. Collectively, these findings identify distinct checkpoint-enriched T cell phenotypic states in SLE, in which immune checkpoint receptor expression coexists with retained effector-associated features. Overall, this work provides a framework for interpreting immune checkpoint-associated T cell phenotypes in systemic autoimmunity.