Fig. 5: Genome-wide CRISPR/Cas9 screening identifies 12 essential direct target genes of NUP98::KDM5A.

A Volcano plot of genome-wide CRISPR/Cas9 screen data from NUP98::KDM5A-expressing cells showing the log2FC and –log10(p-value) values of mean sgRNA abundance at the screen endpoint vs. the sgRNA pool (log2FC > 2.25 and <−2.25, statistical analysis and p-value calculations were performed using MAGeCK). B Intersection of SLAM-seq and genome-wide CRISPR screen data. C Scheme of competition-based proliferation assay (Dox doxycycline, AUC area under curve). D Heatmap representation of proliferation assay data after shRNA-mediated target knockdown (2× shRNAs/gene) showing mean percent of iRFP670-positive cells over 21 days, with positive controls shown at the top and the negative control shown at the bottom (n = 2, biological replicates). E Scatter plot of SLAM-seq and H3K27ac CUT&Tag data showing log2FC values upon dTAG13 (35 nM) treatment compared to DMSO and essential direct target genes are highlighted in color. F Hockey stick plot of H3K27ac CUT&Tag data from primary material of a NUP98::KDM5A PDX model (left). Genes are ranked according to normalized read signal and essential direct target genes are highlighted in color including a quantitative box plot representation (right, essential direct targets n = 12, all genes n = 26,917, two-sided Wilcoxon rank sum test with continuity correction, p-value = 0.0001632). Data are presented as boxplots where the center line represents the median, the bounds of the box indicate the first (25th percentile) and third (75th percentile) quartiles and the whiskers extend to 1.5 × inter-quartile range from the hinges. Data points beyond this range are shown as individual dots and represent outliers. Parts of the figure were created in BioRender. Grebien, F. (2025) https://BioRender.com/n44f632. Source data are provided as a Source Data file.