Fig. 4

TH17/ILC3 gene expression in ALCL and link to the deregulated BATF/BATF3/AP-1 activity. a mRNA expression of TH17/ILC3-associated genes and, as control, GAPDH were analyzed by RT-PCR. b More global approaches to TH17/ILC3 gene expression in ALCL. Upper panels, GSEA of differentially expressed genes between ALCL (K299, SU-DHL-1, DEL, JB6, FE-PD, Mac-2A) and T control (T) cell lines (Jurkat, KE-37, Molt-14, H9) based on TH17 (left) and ILC3 (right) top 100 upregulated genes. Lower panels, PC analyses of ALK⁺ and ALK^– ALCL and T control samples based on 100 top differentially expressed TH17 (left) or ILC3 (right) genes, separating ALCL and T-cell lines along the PC1 axis. PCAs were supplemented by projection of ILC3 samples [45]. n.s., not significant; *P ≤ 0.05; **P ≤ 0.01; ***P ≤ 0.001; ****P ≤ 0.0001. c BATF3 ChIP from K299 cells. Input and precipitated DNA were amplified by qPCR for the indicated promoter or enhancer regions. Combined data of two biological replicates are shown as mean ±  SEM. d Inhibition of AP-1 downregulates TH17/ILC3 genes. Enriched A-Fos or Mock transfected K299 cells were analyzed by RT-PCR for TH17/ILC3 genes. Two (#1 and #2) of four independent experiments are shown. e Analysis of TH17/ILC3 genes in K299 cells with double BATF and BATF3 KO at day 13 following lentiviral transduction. qPCR-based expression of the indicated genes in control cells (CRISPR CTL) or cells transduced with a combination of sgRNAs targeting BATF and BATF3 (BATF + BATF3 DKO). BATF and BATF3 were analyzed to verify their KO. The expression level in CRISPR CTL cells was set 1. Error bars denote 95% CIs. One out of three independent experiments is shown. *P ≤ 0.05; **P ≤ 0.01; ***P ≤ 0.001; n.s., not significant