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[Preprint]. 2024 Jan 10:2023.07.26.550648. Originally published 2023 Jul 29. [Version 2] doi: 10.1101/2023.07.26.550648

Figure 1. Impact of WINi on the transcriptome of MLLr cancer cells.

Figure 1.

(A) Chemical structures of C6 and C16. (B) Crystal structures of C6 or C16 bound to the WIN Site of WDR5 with electrostatic surfaces mapped [PDB IDs: 6E23 (Aho et al., 2019a); 6UCS (Tian et al., 2020)]. The image shows a close-up view of the WIN site. (C) Superimposed WIN site-binding conformations of C6 (green) and C16 (blue). (D) Transcript levels as determined by QuantiGene™ analysis of representative WDR5-bound (color) or non-bound (grayscale) ribosomal protein genes in MV4;11 cells treated with a serial dilution range of either C6 (left) or C16 (right) and relative to DMSO-treated cells (n = 2–3; Mean ±SEM). Vertical dashed line indicates either 2 μM C6 (left) or 100 nM C16 (right). (E) Number of genes with significantly (FDR < 0.05) altered transcript levels following treatment of MV4;11 cells with C6 (2 μM) or C16 (100 nM) for 48 hours, as determined by RNA-Seq (n = 3). See Figure 1—source data 1 for complete output of RNA-Seq analysis. (F) Comparison of gene expression changes elicited by C6 (x-axis) and C16 (y-axis), represented as Log2 fold change (FC) compared to DMSO. WDR5-bound genes are colored red. Locations of RPL22L1 and ZMAT3 are indicated. (G) Overlap of genes with decreased (left) or increased (right) transcript levels in MV4;11 cells treated with C6 or C16. (H) Gene Set Enrichment Analysis (GSEA) showing the distribution of genes suppressed in MV4;11 cells in response to C6 (left) or C16 (right) against the list of all genes bound by WDR5 in those cells (Aho et al., 2019a). NES = normalized enrichment score. (I) Enrichment analysis of genes suppressed (left) or induced (right) by C6 or C16 in MV4;11 cells. KEGG and Hallmark.MSigDB pathways are shown. Fold enrichment of indicated pathways is presented on the x-axis, the number of genes is shown in italics in each bar, and colors represent −Log10 FDR. See Figure 1—source data 2 for additional GSEA (Hallmark) and ORA (Hallmark) analyses of differentially expressed genes. (J) Transcript level changes in WDR5-bound (left) and non-bound (right) RPGs elicited by C6 (top) or C16 (bottom).