Fig. 3: Rapid, environment-dependent rewiring of Treg gene expression programs after BMT.

a UMAP embedding of donor Treg either after in vitro expansion before transfer (“Donor”), or re-isolated from recipient organs 7 days after transfer, as well as tissue-resident CD62L⁺ (naïve) and CD62L⁻ (effector/memory) Treg from non-transplanted animals, analyzed by RNA-seq and colored by their origin. Unlike spleen and liver, colon harbors only CD62L⁻ Treg. Data are from two independent experiments per BMT group (with n = 3 animals/experiment receiving the same graft). b Scatter plot of global gene expression (logCPM > 1, logRPKM > 1) comparing donor Treg (after BMT, with or w/o Tconv) re-isolated from colon versus non-colon samples. Differential genes are highlighted by coloring (p_adj.|FC|>1.5 > 0.05, qlf-test). NLT and LT signature genes defined by Miragaia et al.³⁰ are highlighted. c Barcode plots presenting GSEA results for the indicated gene lists across the logFC ranking of genes based on the comparison shown in (b). Enrichment p values of two-sided rotation gene set tests are given. d Main component of the gene co-expression network generated with Graphia (r ≥ 0.845, k-NN with k = 4, descending rank order, Louvain cluster granularity 0.6). For each co-expression cluster the top enriched functional annotation is given (except for cluster 7). More detailed functional annotation is provided in Supplementary Fig. 3m. e Heatmap presenting hierarchically clustered (sample-wise) and scaled expression data of genes included in the network shown in (d). Samples are color-coded as in (a). f Heatmap presenting averaged and scaled expression data of transcription factor genes associated with individual co-expression clusters. b, c, e, f Source data are provided as a Source Data file.