Human naïve regulatory CD4 T cell identity: Transcriptional and chromatin determinants

Abstract Human naïve regulatory CD4 T cells (Tregs) are a thymus-derived population essential for peripheral tolerance and tissue homeostasis, yet the mechanisms that preserve their steady-state identity remain poorly understood. Naïve Tregs co-express two superimposed programmes: Treg lineage and naïve T-cell identity. We resolved this entanglement into orthogonal programmes by confronting transcription and chromatin accessibility profiles across thymic, naïve, and memory Treg and conventional CD4 T-cell populations. The core Treg programme, comprising 293 genes common to all three compartments, revealed a conserved regulatory architecture with AP1/ETS members organising gene regulatory modules. The lineage-independent naïve programme identified 175 genes peaking specifically in naïve cells, with overrepresentation analysis supporting translational preparedness as a naïve hallmark alongside cell trafficking, and POU2F1/OCT1 emerging as key regulator. KLF/SP factors provided quantitative fine-tuning to both programmes. These findings establish a two-programme model of human naïve Treg identity with implications for immune senescence and Treg-based cell therapies.