Figure 3.
Increased upregulation of genes involved in differentiation with IGF2BP3 knockdown and menin-MLL inhibition in MLL-Af4 leukemia. (A) Volcano plots of differentially expressed genes with IGF2BP3 knockdown (top) and with MI-503 treatment (left) in MLL-Af4 Lin– NT cells, using DESeq analysis on RNA-sequencing samples from MLL-Af4 Lin– NT or I3KO cells treated with MI-503 1.0 μM or DMSO vehicle. (B) Venn diagram of shared differentially expressed genes with IGF2BP3 knockdown and MI-503 treatment in MLL-Af4 Lin– NT cells. (C) Volcano plots of differentially expressed genes with IGF2BP3 knockdown (top) and with MI-503 treatment (left) in MLL-Af4 Lin– I3KO cells, using DESeq analysis on RNA-sequencing samples from MLL-Af4 Lin– NT or I3KO cells treated with MI-503 1.0 μM or DMSO vehicle. (D) Overlap between differentially expressed genes with MI-503 in MLL-Af4 Lin– NT or I3KO cells and with IGF2BP3 knockdown and known MLL-AF4 ChIP targets from previously published data sets in SEM and RS4;11 and known IGF2BP3 eCLIP targets from previously published data sets of MLL-Af4 CD11b+ and MLL-Af4 Lin– cells. P values calculated using Fisher exact test. (E) Pathway enrichment for upregulated genes with IGF2BP3 knockdown using Metascape analysis webtool on MLL-Af4 Lin− IGF2BP3 DESeq data set with an adjusted P < .05 cutoff. (F) Pathway enrichment for upregulated genes with MI-503 treatment using Metascape analysis webtool on MLL-Af4 Lin− NT MI-503 DESeq data set with an adjusted P < .05 cutoff. FC, fold change.

Increased upregulation of genes involved in differentiation with IGF2BP3 knockdown and menin-MLL inhibition in MLL-Af4 leukemia. (A) Volcano plots of differentially expressed genes with IGF2BP3 knockdown (top) and with MI-503 treatment (left) in MLL-Af4 Lin– NT cells, using DESeq analysis on RNA-sequencing samples from MLL-Af4 Lin– NT or I3KO cells treated with MI-503 1.0 μM or DMSO vehicle. (B) Venn diagram of shared differentially expressed genes with IGF2BP3 knockdown and MI-503 treatment in MLL-Af4 Lin– NT cells. (C) Volcano plots of differentially expressed genes with IGF2BP3 knockdown (top) and with MI-503 treatment (left) in MLL-Af4 Lin– I3KO cells, using DESeq analysis on RNA-sequencing samples from MLL-Af4 Lin– NT or I3KO cells treated with MI-503 1.0 μM or DMSO vehicle. (D) Overlap between differentially expressed genes with MI-503 in MLL-Af4 Lin– NT or I3KO cells and with IGF2BP3 knockdown and known MLL-AF4 ChIP targets from previously published data sets in SEM and RS4;11 and known IGF2BP3 eCLIP targets from previously published data sets of MLL-Af4 CD11b+ and MLL-Af4 Lin– cells. P values calculated using Fisher exact test. (E) Pathway enrichment for upregulated genes with IGF2BP3 knockdown using Metascape analysis webtool on MLL-Af4 Lin− IGF2BP3 DESeq data set with an adjusted P < .05 cutoff. (F) Pathway enrichment for upregulated genes with MI-503 treatment using Metascape analysis webtool on MLL-Af4 Lin− NT MI-503 DESeq data set with an adjusted P < .05 cutoff. FC, fold change.

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