Extended Data Fig. 10: Prime editing scanning screen for EGFR activation identifies enriched variants conferring EGF-independent growth.
From: Multimodal scanning of genetic variants with base and prime editing
(a) Scatter plot representing the LFCs of individual pegRNAs between the nontreated and EGF-deprived arms of the screen for each mutation category. Intended edits can be introduced along with an additional synonymous mutation (intended + synonymous). For each of these, additional control pegRNAs introducing only the intended edit (intended edit only) or the synonymous mutation (synonymous only) are also added to the library. Some edits can correspond to both intended and synonymous mutations (both intended and synonymous). (b) Volcano plot showing the LFCs and negative-log FDR of individual pegRNAs between nontreated and EGF-deprived cells. Colors represent the clinical significance of the corresponding variants. (c) Scatter plot showing the LFCs of individual pegRNAs between nontreated and EGF-deprived cells along the EGFR protein. Colors denote the most prevalent tissues for each variant as reported in the COSMIC database. (d) Scatter plot comparing the LFCs of pegRNAs introducing the same intended edit with or without additional synonymous mutation. Only pegRNAs with matching spacers and primer binding site (PBS) lengths are shown. The pegRNAs with a -log10(FDR) > 2 in either category are shown in red. (e) Deep sequencing data for individual pegRNA validation. PEmax-expressing MCF10A∆MLH1 cells were infected with the indicated pegRNAs in three biological replicates (n = 3) and later split into control and treatment arms deprived of EGF. The percentages of reads correspond to perfect edits, including additional synonymous mutations. The P values are shown for two-sided t-tests between nontreated and EGF-deprived samples.
