Figure 2. IRF8 is enriched at the MEF2D locus and modulates MEF2D expression.

(A) RNA-seq analysis of gene expression changes in MOLM-13-dIRF8 cells treated with either DMSO or 500 nM of dTAG-47 for 4 h. Genes are ranked by log₂ fold change (n = 3).

(B) ESs of top 12 downregulated genes from DEPMAP dataset with log₂ fold change less than —0.5 in IRF8-expressed (TPM > 1) AML cell lines (n = 12). Shown is a box and whisker plot of copy-number-adjusted ESs (CERES). TPM, transcripts per million reads.

(C) Scatterplot of IRF8 and MEF2D essentiality scores in 33 human cancer cell lines extracted from Lu et al. (2018). IRF8^hi cell lines are labeled. r, Pearson’s correlation coefficient.

(D) RNA-seq analysis of gene expression changes in indicated cell lines transduced with sgIRF8 or sgNeg for 4 days. sgNeg and two independent sgRNAs targeting IRF8 are used (n = 2 biological replicates per sgRNA). Ranking position from the top most downregulated gene is indicated in parentheses.

(E) GSEA rank plot of RNA-seq data presented in (D). The MEF2D signature is defined as the top 200 downregulated genes upon MEF2D depletion. Normalized enrichment score (NES) and false discovery rate (FDR) q value are shown.

(F) Unbiased GSEA using all signatures from MSigDB v6.1 (Liberzon et al., 2015), together with the MEF2D signature for RNA-seq data presented in (D). Each gene set is represented as a single dot. The MEF2D signature is indicated in red, with numeral rank from the top most-enriched gene set in parentheses.

(G) RNA-seq analysis of gene expression changes in MEF2D-depleted MOLM-13 cells 5 days after transduction of sgNeg or sgMEF2D. Two independent sgRNAs targeting either MEF2D or a negative control locus were used. MEF2D signature genes are indicated with a red box.

(H) Metaplot (top) and density plot (bottom) showing enrichment of IRF8 and H3K27ac surrounding the 23,429 IRF8 ChIP-seq peaks at a ±5-kb interval in MOLM-13 cells. Peaks were ranked by IRF8 ChIP-seq tag counts.

(I) Gene tracks of H3K27ac and IRF8 enrichment at the MEF2D locus in the indicated leukemia cell lines. H3K27ac and IRF8 ChIP-seq tracks in THP-1 cells are extracted from GSE123872.

See also Figure S2 and Table S1.