Spatiotemporal lineage recording of tumor immune escape with eTRACER

We introduce eTRACER, a novel CRISPR-Cas9 lineage tracer that targets neutral 3’ untranslated regions (3’UTR) of high-expression endogenous genes, enabling efficient recovery of static and evolving barcodes from single-cell and spatial transcriptomics. By optimizing gradient editing efficacy and avoiding large disruptive deletions, eTRACER reconstructs high-fidelity and high-resolution single-cell phylogenies. We applied eTRACER to systematically decode clonal and phenotypic fate maps of EGFR-mutant LUAD under CD8+ T cell-mediated cytotoxicity in mice. Briefly, we have provided here processed datasets from eTARCER lineage tracing, scRNA-seq, spatial transcriptomics, and single cell multiome data. Scripts for reproducing our results are available in the reproducibility repository on GitHub: https://github.com/liangzhenhou/eTRACER