Extended Data Fig. 8: Transcriptomic and epigenetic evaluation of AHR activation in T cells and association with AP-1 family members.

a, Schematic of RNA-Seq time course experiment to identify early transcriptomic events of AHR modulation. b, PCA plots of RNA-seq samples after 12 h (left) and 48 h (right) of stimulation with TGF-β and either AHR agonist (TCDD) or AHR inhibitor (AHRinh) CH-223191. c,d, Volcano plots of DESeq2 results from RNA-Seq analysis of memory CD4⁺ T cells cultured for 12 h (c) and 48 h (d) in TGF-β and either TCDD or AHRinh. The samples used for DESeq2 analysis correspond with the PCA plots in b. e, Pathway enrichment analysis of genes upregulated in TCDD-treated CD4⁺ T cells at 48 and 72 h of culture, based on Elsevier pathway collection. f, Transcription factor enrichment analysis of samples at 12 h using EnrichR databases TRRUST Transcription factors 2019 (left) and EnrichR Transcription factor Co-occurence (right). g, AHR CUT&RUN binding signal (top) and heat map (bottom). h, Volcano plot of AHR CUT&RUN Diffbind analysis comparing samples with and without AHR CRISPR knockout (top) and HOMER motif analysis of all upregulated peaks found in AHR WT samples (bottom). i, Representative AHR binding regions. j, Comparison of AHR binding in cells treated with AHR agonist or AHR antagonist. k, Venn diagram of overlapped genes bound by AHR with Th22 signature genes as shown in Fig. 1e, hypergeometric P-value is shown. l, Pathway enrichment analysis of AHR-bound peak associated genes. TCDD = AHR agonist; AHRinh = AHR inhibitor, CH-223191. Panel a created with Biorender.com.