Single-cell transcriptomic analysis reveals disparate effector differentiation pathways in human Treg compartment

Abstract

Human FOXP3+ regulatory T (Treg) cells are central to immune tolerance. However, their heterogeneity and differentiation remain incompletely understood. Here we use single-cell RNA and T cell receptor sequencing to resolve Treg cells from healthy individuals and patients with or without acute graft-versus-host disease (aGVHD) who undergo stem cell transplantation. These analyses, combined with functional assays, separate Treg cells into naïve, activated, and effector stages, and resolve the HLA-DRhi, LIMS1hi, highly suppressive FOXP3hi, and highly proliferative MKI67hi effector subsets. Trajectory analysis assembles Treg subsets into two differentiation paths (I/II) with distinctive phenotypic and functional programs, ending with the FOXP3hi and MKI67hi subsets, respectively. Transcription factors FOXP3 and SUB1 contribute to some Path I and Path II phenotypes, respectively. These FOXP3hi and MKI67hi subsets and two differentiation pathways are conserved in transplanted patients, despite having functional and migratory impairments under aGVHD. These findings expand the understanding of Treg cell heterogeneity and differentiation and provide a single-cell atlas for the dissection of Treg complexity in health and disease.

Natural Barcodes for Longitudinal Single Cell Tracking of Leukemic and Immune Cell Dynamics

“…Although progress in these directions has been made (75,100,138), the envisioned efforts are still in their infancy. Single-cell transcriptomics are currently underway to describe immune cell populations implicated in GvHD such as B cells (139), regulatory T cells (140), or cytotoxic CD4 + T cells (141). In the latter example, the authors tracked expansion of a mutation in the mTOR gene within donor-derived T cells which they associate with persistent immune activation and GvHD.…”

Rebooting Regulatory T Cell and Dendritic Cell Function in Immune-Mediated Inflammatory Diseases: Biomarker and Therapy Discovery under a Multi-Omics Lens

“…Although not an IMID per se, graft-versus-host disease (GVHD) manifests as an autoimmune disease, and transcriptomic approaches have been employed to dissect Treg complexity in patients receiving hematopoietic stem cell transplantation [ 71 ]. Specifically, single-cell transcriptomic analysis was performed in Tregs of the peripheral blood and bone marrow of healthy donors and patients after hematopoietic stem cell transplantation that were either experiencing GVHD or not.…”

“…Pseudotime trajectory analysis uncovered the transition among clusters according to which naïve Tregs followed two distinct differentiation pathways towards either Foxp3 hi Tregs (Path 1) or MKI67 hi Tregs (Path2). Whereas similar clusters, spanning from naïve to activated/effector Tregs, were identified in all groups, effector Tregs clusters in individuals developing GVHD displayed downregulation of suppression and migration pathways as well as a senescence-like signature compared with non-GVHD patients [ 71 ]. Although the latter can be attributed to the age gap between GVHD and non-GVHD patients, Treg interrogation on a single-cell level offered a greater understanding of Treg features upon GVHD.…”

Induced Human Regulatory T Cells Express the Glucagon-like Peptide-1 Receptor

“…Apart from being CD4 + CD25 + FoxP3 + , Treg cells are highly heterogeneous. Thus, 9 and 22 distinct subpopulations of human Treg cells have been identified by single-cell transcriptomic analysis and mass cytometry, respectively [ 18 , 19 ].…”