Extended Data Fig. 4: Transcriptomic analysis of spleen and CNS Treg cells in EAE peak and recovery stages.

Volcano plots displaying differentially expressed genes (≥1.5-fold, adjusted P value < 0.05) between recovery (Rec) and peak CNS Treg cells (a), peak CNS and peak spleen (SPL) Treg cells (b), and recovery CNS and SPL Treg cells (c). Adjusted P values in (a-c) are derived from DESeq2 using a two-tailed Wald’s test with correction for multiple testing using the Benjamini and Hochberg method (peak n = 4, recovery n = 5 biological replicates). Labeled genes comprise a selection of genes commonly associated with non-nonlymphoid tissue Treg cells (black: not significantly regulated, orange: DEG, light grey: not significant and not part of the selection of tissue Treg cell genes). (d) Summary of gene set enrichment analyses comparing recovery and peak CNS Treg cells using the MSigDb Hallmark gene set collection. (e, f) Enrichment plot of genes part of the ‘TNFα-signaling via NFκB’ (e) and the ‘IL-2 STAT-5 signaling’ signature (FDR, false discovery rate; NES, normalized enrichment score) (f). (g-h) Heatmap and hierarchical clustering of significantly upregulated genes (≥1.5-fold, adjusted P value < 0.05) that contribute to the leading-edge genes for the gene sets ‘TNFα-signaling via NFκB’ (g) and ‘IL-2 STAT-5 signaling’ (h) in recovery (Rec) vs. peak CNS Treg cells.