Allospecific splenic Tr1 cells drive effector T cell exhaustion through upregulated Areg-EGFR signaling to promote transplant tolerance

Inducing stable tolerance to transplants remains a challenge in immunology. Previously, we induced tolerance to allogeneic islets in nonhuman primates by preemptive alloantigen delivery to antigen-presenting cells in situ. Here, mass cytometry phenotyping with incorporated donor-derived MHC-I peptide-loaded MHC-II tetramers revealed accumulation of allospecific CD4+ T cell clusters in the spleen of tolerant recipients. Areg+Tr1 regulatory and terminally exhausted EGFRhi T (Tex) cells represented the predominant allospecific subsets. Trajectory analysis showed that antigen-experienced effector memory T cells differentiated into suppressive Areg+Tr1 and EGFR+TOX+Nur77+TCF-1- Tex subsets. Cell-cell communication mapping showed that exhausted and effector memory T cells engaged with allospecific Tr1 cells via the Areg-EGFR axis. Gene silencing studies confirmed that Tr1 cells utilize Areg-EGFR signaling to drive the metabolic suppression and epigenetic reprogramming of CD4⁺ T cells through a Nur77-dependent pathway. These findings point to the splenic Areg⁺Tr1 cell-EGFR⁺Teff cell axis as a critical immunoregulatory pathway in peripheral transplant tolerance.

Here we provide the raw and processed CyTOF (mass cytometry by time of flight) data and R analysis scripts used to arrive at these conclusions for each cell type mentioned above. CyTOF data is provided as FCS-format files representing counts for thousands of cells and up to 36 mass-tagged protein markers.

Methods
Raw FCS files were transformed and converted to Seurat objects with custom R scripts (process_raw_X.txt and make_seurat_X.txt files, respectively) using information contained in sample key files (sample_ref_X.txt files). These data are separated into folders comprising the data files and analysis files for each respective cell type group.