Fig. 6: Comparative analysis of prime editing and cDNA screening datasets of TP53 variants reveals pathogenic variants in the OD.
From: High-throughput evaluation of genetic variants with prime editing sensor libraries

a, Scatterplot of prime editing Z-score for pegRNAs ≥10% editing at D34 in the Nutlin-treated condition, and the corresponding cDNA variant Z-score in the p53-WT background in the presence of Nutlin, colored by p53 domain. b, cDNA (red) and prime editing (blue) Z-scores for pegRNAs/variants located in the OD. The pegRNA with the highest Z-score is labeled. c, The difference in Z-scores between prime editing and cDNA screens (∆Z-score) for pegRNAs ≥10%, separated by p53 domain. OD versus DBD (P = 6.025 × 10−85), versus PRR (P = 1.396 × 10−26), and versus TAD (P = 3.684 × 10−15). d, Boxplot of the Z-scores for variants in the cDNA and prime editing screens (P = 1.192 × 10−6), considering only the most efficient pegRNA for each variant. Statistics for c and d shown for two-sided t-test with Bonferroni correction. *P ≤ 0.05; **P ≤ 0.01; ***P ≤ 0.001; ****P ≤ 0.0001; NS, not significant (P > 0.05). In all boxplots (c and d), boxes indicate the median and IQR for each sample with whiskers extending 1.5× IQR past the upper and lower quartiles. All Z-scores were calculated from the LFC of each pegRNA, in turn calculated using MAGeCK from the median values across n = 3 biologically independent samples. e, Visualization of the residue-averaged ∆Z-scores on an NMR-structure of p53 OD (PDB: 1OLG). f, Scatterplot of the cDNA Z-score of TP53 variants and the corresponding ∆RFP% of cDNAs tested with competition assays. g, Comparison of the ∆RFP% for cDNAs (D10) and corresponding pegRNAs (D14) for variants tested with competition assays. Points marked with ‘X’ indicate a replicate with an insufficient viable cell count (<500) to determine the RFP+%. In this case, the RFP+% was quantified as unchanged from the previous timepoint for the matched replicate. n = 3 biologically independent replicates performed per condition. Data are presented as mean values with a 95% confidence interval. Source data and code to reproduce this figure can be found at https://github.com/samgould2/p53-prime-editing-sensor/blob/main/figure6.ipynb. EV, empty vector control; WT, wild type TP53 control.