Systematic comparison of CRISPR/Cas9 and RNAi screens for essential genes

Abstract

We compared the ability of short hairpin RNA (shRNA) and CRISPR/Cas9 screens to identify essential genes in the human chronic myelogenous leukemia cell line K562. We found that the precision of the two libraries in detecting essential genes was similar and that combining data from both screens improved performance. Notably, results from the two screens showed little correlation, which can be partially explained by the identification of distinct essential biological processes with each technology.

Figure 1. Parallel shRNA and CRISPR/Cas9 deletion screens to identify essential genes in K562

(a) Schematic of screen. shRNA and Cas9 libraries were lentivirally infected into K562 and selected via puromycin treatment. After this time zero, replicate cell populations were maintained in log phase growth for two weeks. Library representation at each time point was monitored by deep-sequencing of the inserted locus. (b) ROC curves indicate screen performance in identifying essential genes by comparing the library composition between the plasmid library and cells after two weeks growth. True positive rates and false positive rates were calculated using a previously established gold standard set of essential and nonessential genes. ROC curves for Cas9 (red) and shRNA (blue) screens based on the median score averaged over two replicates. Alternatively, data from single replicates of both Cas9 and shRNA screens were combined using casTLE (purple). (c) The number of essential genes at 10% false positive rate and their overlap based on the average median data from Cas9 and shRNA screens, as well as combination of a single replicate from both screens using casTLE. False positive rate was estimated using gold standard nonessential genes.

Figure 2. Differences between Cas9 and shRNA results

(a) Comparison of casTLE scores between single replicates of Cas9 and shRNA data. A large positive casTLE score indicates a high confidence increase in growth rate, while a highly negative casTLE score indicates a high confidence decrease in growth rate, i.e. essential. Density is in log scale. (b) casTLE scores are shown for gold standard essential and nonessential genes. (c) Adjusted p-values for select GO terms for shRNA and Cas9 screens as well as for data from both screens combined with casTLE. (d) casTLE scores shown for genes involved in the respiratory chain complex (GO:0098803) and the chaperonin-containing T-complex (GO:0005832), which exhibit differential enrichment in Cas9 and shRNA screens.