Extended Data Fig. 8: BATF and IRF4 binding and gene expression changes in pMIG-, HKE-, and BATF-transduced cells.
From: BATF and IRF4 cooperate to counter exhaustion in tumor-infiltrating CAR T cells
a, Contour plot relating BATF ChIP-seq signals (log2(CPM)) in BATF-transduced CD8+ T cells to signals from the corresponding peaks in pMIG-transduced cells. b, Left, Distribution of BATF ChIP-seq reads in peaks in BATF-transduced cells (red) versus pMIG-transduced cells (black). Right, BATF ChIP-seq signal distribution in the ‘BATF and pMIG’ peaks common to the two conditions (blue) and in ‘BATF-new’ peaks observed only in BATF-transduced cells (red). The BATF-new peaks defined here are largely the same as the BATF-only peaks in Fig. 6a. c, Heatmaps of the IRF4 ChIP-seq signal in BATF-transduced, BATF-HKE-transduced, and pMIG-transduced cells, at IRF4 peak locations called in BATF-transduced cells. Curves at the top show the average signal taken over all peaks in the respective heatmap. d, Heatmaps of the BATF ChIP-seq signal in BATF-transduced, BATF-HKE-transduced and pMIG-transduced cells, at IRF4 peak locations called in pMIG-transduced cells. Curves at the top show the average signal taken over all peaks in the respective heatmap. e, Genome browser view of Ctla4 gene locus showing BATF and IRF4 ChIP-seq signals from pMIG-, BATF-, and HKE-transduced CD8+ T cells. f, Heatmap of normalized RNA-seq reads (as z-scores) under the indicated conditions, for the top 100 genes differentially expressed after αCD3/αCD28 stimulation of pMIG-transduced cells. Data obtained from two or three biological experiments.
