BASELINE: A CRISPR base editing platform for mammalian-scale single-cell lineage tracing
Evan Winter, Francesco Emiliani, Aidan Cook, Asma Abderrahim, Aaron McKenna
CRISPR-based recording technologies are a promising solution to map cell lineage in conjunction with single-cell profiling. We introduce BASELINE, a technique employing base editing to create detailed lineage maps alongside single-cell analysis.
BASELINE uses the Cas12a adenine base editor to irreversibly edit nucleotides within 50 synthetic target sites integrated multiple times into a cell’s genome. The system accumulates lineage-specific marks over a wide range of biologically relevant intervals, recording more than 4,300 bits of information in a model of pancreatic cancer — a 50X increase over existing technologies.
Single-cell sequencing reveals high-fidelity capture of these recorders, recovering lineage reconstructions up to 40 cell divisions deep, within the estimated range of mammalian development. BASELINE demonstrates applicability to developmental and disease research scenarios where conventional approaches face engineering constraints.