Genome-wide CRISPR/Cas9 screening with InO in the NALM-6 cell line (passage 10). (A) Volcano plots showing InO sensitization (negatively selected, in blue) and resistance (positively selected, in red) genes by CRISPR/Cas9 screening. (B) GSEA of negatively enriched pathways. Magma colors and size of the dots represent the normalized enrichment score (NES) and −log10 false discovery rate (FDR) q-values of the top 20 negatively enriched pathways, respectively. The respective gene set members of each pathway are denoted by a bubble plot. Viridis colors and size of the dots represent running enrichment score and −log10 of CRISPR/Cas9 P value respectively. (C) Log2 FC values of sgRNAs targeting the top 10 InO resistance genes. Each gray line represents an individual sgRNA and the central dotted line represents the median log2 FC of the sgRNAs (∼0). Each red line represents the sgRNA of the target gene. Multiple sgRNAs targeting each of the top 10 genes (including CD22) were significantly enriched by inotuzumab, showing an on-target gene knockout by CRISPR/Cas9. (D) DNTT RNA expression in paired patient samples compared with pre- and post-InO. The plot represents the mean ± standard error of the mean for each group. P = .03 by two-tailed paired t test. Samples belonging to the same patient were connected using lines. CPM, counts per million FC, fold change; GSEA, gene set enrichment analysis; sgRNAs, single-guide RNAs.