Paper

Activity-based selection for enhanced base editor mutational scanning

Steger, Ryan J, Drepanos, Laura M, Reint, Ganna, Shah, Spencer T, Doench, John G, Griffith, Audrey L, Kaplan, Eleanor G

2024

Overview

Base editing is a CRISPR-based technology that enables high-throughput, nucleotide-level functional interrogation of the genome, which is essential for understanding the genetic basis of human disease and informing therapeutic development. Base editing screens have emerged as a powerful experimental approach, yet significant cell-to-cell variability in editing efficiency introduces noise that may obscure meaningful results. Here, we develop a co-selection method that enriches for cells with high base editing activity, substantially increasing editing efficiency at a target locus. We evaluate this activity-based selection method against a traditional screening approach by tiling guide RNAs across TP53, demonstrating its enhanced capacity to pinpoint specific mutations and protein regions of functional importance. We anticipate that this modular selection method will enhance the resolution of base editing screens across many applications.Competing Interest StatementJGD consults for Microsoft Research, BioNTech, PhenomicAI, Servier, and Pfizer. JGD consults for and has equity in Tango Therapeutics. JGD serves as a paid scientific advisor to the Laboratory for Genomics Research, funded in part by GSK; and the Innovative Genomics Institute, funded in part by Apple Tree Partners. JGD receives funding support from the Functional Genomics Consortium: Abbvie, Bristol Myers Squibb, Janssen, and Merck. JGD interests are reviewed and managed by the Broad Institute in accordance with its conflict of interest policies. A patent application related to this work has been filed.

• Publisher: Cold Spring Harbor Laboratory Press,Cold Spring Harbor Laboratory
• Subject: CRISPR / Editing / Genetics / Genomics / Medical innovations / p53 Protein / Patent applications