Fig. 3: CRISPR-Cas9 essentiality screens reveal preferential dependency of MLL–MEN1 in EZH2-mutated DLBCL. | Nature Communications

Fig. 3: CRISPR-Cas9 essentiality screens reveal preferential dependency of MLL–MEN1 in EZH2-mutated DLBCL.

From: Context-defined cancer co-dependency mapping identifies a functional interplay between PRC2 and MLL-MEN1 complex in lymphoma

Fig. 3: CRISPR-Cas9 essentiality screens reveal preferential dependency of MLL–MEN1 in EZH2-mutated DLBCL.The alternative text for this image may have been generated using AI.

a A schematic diagram showing the workflow of chromatin-focused CRISPR-Cas9 essentiality screen (EpiLib screen) in DLBCL cell lines. Created by BioRender. b Scatter plot showing MLL1, MEN1, and PRC2 complex members are highly essential to DLBCL cell line KARPAS422 (K422) in both EpiLib screen and the genome-wide CRISPR-Cas9 essentiality screen from DepMap. p-value was determined by one-way ANOVA. c Violin plots showing the significant differences in dependency between genes in module #8 (n = 14 and 12 genes for DepMap and EpiLib screens, respectively) and other genes (n = 16,840 and 553 genes for DepMap and EpiLib screens, respectively) in DepMap screen (left) and EpiLib screen (right) in EZH2 mutant KARPAS422 (K422) cells. Lower gene effect score indicates that a gene is more likely to be essential. The center line in the embedded boxplots represents the median, the box limits are the 25th and 75th percentiles, and the whiskers are the minimum to maximum values. P values were determined by unpaired two-tailed Student’s t-test. For statistical analyses of DepMap and EpiLib screens, p = 2.38e−4 and 0.0267, respectively. d Negative-selection competition assay measuring the relative percentage of RFP+/sgRNA-positive cells over time after transduction of EZH2 mutant DLBCL cell lines KARPAS422 and SuDHL4 with control or MEN1 sgRNAs. n = 3 independent experiments. Dots and whiskers are mean ± s.d. P values were determined by paired two-tailed Student’s t-test. For statistical analyses of KARPAS422 sgMEN1-1/−2, p = 8.24e-6 and 1.54e−6, respectively. For statistical analyses of SuDHL4 sgMEN1-1/−2, p = 1.11e−5 and 3.18e-6, respectively. e Incidence of xenograft tumor formation after injection of KARPAS422 cells transduced with control or MEN1 sgRNAs. P values were determined by Fisher’s exact test. For statistical analyses of sgMEN1-1/−2, p = 3.53e−6 and 1.54e−14, respectively. The experiments contain 12 injections for each condition and are not repeated. f Relative percentage of viable cells after 8-day treatment of MEN1 inhibitor MI503 with indicated dosage (left) and measured IC50 (right) for EZH2-mutant and -wildtype DLBCL cell lines. n = 3 independent experiments. Dots and whiskers are mean ± s.d. P values were determined by unpaired two-tailed Student’s t-test. For statistical analyses of IC50, p = 0.0488. g Relative percentage of viable cells after 4-day treatment of MEN1 inhibitor VTP50469 with indicated dosage for H3K27me3-high (RPMI-8226) and H3K27me3-low (MM.1S) multiple myeloma cell lines. n = 3 independent experiments. Dots and whiskers are mean ± s.d. *p < 0.05; **p < 0.01; ***p < 0.001. Source data are provided as a Source Data file.

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