Fig. 4: NRF2 regulates expression of the prostacyclin receptor PTGIR.
From: The prostacyclin receptor PTGIR is a NRF2-dependent regulator of CD8+ T cell exhaustion
a, Schematic of RNA-seq workflow for WT or Keap1−/− P14 T cells (CD45.2+) responding to LCMV Armstrong infection. P14 T cells were sorted via CD45.2+ selection at 7 d.p.i. (three biological replicates or genotypes). b, Volcano plot highlighting differentially expressed genes (DEGs) in WT and Keap1−/− P14 T cells at 7 d.p.i. with LCMV Armstrong. The x axis shows log2(fold-change) (log2(FC)) (Keap1−/− or WT) and the y axis −log10(FDR). Gray- and blue-shaded regions represent genes significantly enriched (−log10(FDR) > 1.30, corresponding to FDR < 0.05) in WT and Keap1−/− P14 T cells, respectively. Blue circles highlight conventional NRF2 targets from the NFE2L2.V2 gene set (M2870). Ptgir is shown in red. c, Relative expression levels of Nqo1 and Ptgir mRNA (normalized to Actb) in WT and Keap1−/− P14 T cells isolated from LCMV-infected mice (7 d.p.i.) as determined by qPCR (n = 3 mice per group). d,e, Relative expression of mRNA (d) and protein (e) levels for NAD(P)H quinone dehydrogenase 1 (Nqo1/NQO1) and Ptgir/PTGIR in activated WT and Keap1−/− P14 cells after CRISPR–Cas9 editing using control (sgScr) or Nfe2l2-targeting (sgNfe2l2) sgRNAs. RNA levels were normalized to Actnb. Protein levels were normalized relative to ACTN4 levels (n = 3 replicates per group). f, Data tracks for NRF2 peak enrichment at Ptgir (top) and Nqo1 (bottom) gene loci in mouse cells using NRF2 ChIP–seq. Left, NRF2 peak enrichment in Keap1−/− MEFs as determined by NRF2 ChIP–seq (accession no. GSE87357, ref. 31). Right, NRF2 peak enrichment in CD8+ T cells expressing a constitutively active form of NRF2 (CA-NRF2) (accession no. GSE224756, ref. 32). Data tracks for NRF2 ChIP–seq and input samples are shown. Data are indicated as mean ± s.e.m. (c) or mean ± s.d. (d and e) for technical replicates from a representative experiment. Statistical significance was calculated via Student’s t-test (c) or one-way ANOVA with Tukey’s test (d and e). NS, P ≥ 0.05; *P = 0.05; **P = 0.01; ***P = 0.001; ****P = 0.0001.
