A systematic transcriptomic atlas and predictive framework for metabolite-driven T cell state transitions

Abstract

Summary Gut microbial and endogenous metabolites are key regulators at the interface of host metabolism and immunity, yet their global effects on human T cell states remain poorly defined. Here, we profile primary human T cell responses to 364 endogenous and microbiota-derived metabolites using high-throughput digital RNA with perturbation of genes sequencing (DRUG-seq), revealing structured transcriptional trajectories spanning baseline, metabolically primed, and highly activated states. We develop DRUG-seq-PerturbFormer, a multi-task deep learning framework that quantitatively captures perturbation magnitude and directionality across these states. This analysis identifies a subset of metabolites that robustly reprogram T cell transcriptional programs. In a dextran sulfate sodium (DSS)-induced colitis model, representative candidates attenuated disease severity and were associated with suppression of inflammatory programs and partial restoration of immune homeostasis. Collectively, these findings show that metabolites act as signals shaping T cell function via transcription, nominating immunomodulatory targets for inflammatory diseases.