CD4 T-cells include effector/conventional (Tconv) and suppressive/regulatory (Treg) lineages with thymus origin that egress into naïve (n) compartment with broad-reactivity, and are continuously challenged to differentiate into memory (m) T-cells upon contact with cognate antigens. Naïve compartment homeostasis is, therefore, critical to ensure T-cell diversity, depending on homeostatic proliferation to counteract differentiation/death rates and thymic replenishment decline. Intriguingly, adults thymectomised early in life feature nTreg preservation despite remarkable nTconv contraction. Here, we aim to identify molecular pathways regulating human naïve Treg and Tconv homeostasis.
We used CD25/CD127 to sort Tregs/Tconvs from CD4 single-positive thymocytes (3 thymuses discarded during pediatric corrective cardiac surgery), and from circulating naïve and memory CD4 T-cells (3 healthy young adults). Transcriptomes were generated by RNA-seq and differential expressions quantified at gene level (DEG) for each lineage along sequential transitions between compartments, thymus-to-naïve (TN) and naïve-to-memory (NM).
We find a large consistency between Tregs and Tconvs for expression changes upon thymus egress (TN: 3663 of 4351) and during memory differentiation (NM: 446 of 970), in agreement with a common developmental programme. However, there is also significant DEG specific to each lineage in TN and NM transitions (respectively: Tregs, 406/374; Tconvs, 276/141). Importantly, some genes are specifically upregulated in nTregs upon thymic egress and repressed after mTreg differentiation. Amongst these is FOXP1-AS1, a quiescence regulator, suggesting a Treg-specific mechanism of promoting cell growth in naïve compartment by silencing pathways that inhibit proliferation.
Exploring distinct pathways of naïve Treg and Tconv homeostasis may identify novel targets to modulate immune reconstitution.