High-resolution spatial mapping of cell state and lineage dynamics in the tumor microenvironment with PEtracer 2302205

Abstract Introduction The tumor microenvironment is a complex ecosystem of cancer, immune, and stromal cells. Within this environment, cancer progression is coordinated by both cell-intrinsic and -extrinsic factors. Targeting signaling interactions between cancer and immune cells has proven to be an effective therapeutic strategy, as evidenced by the remarkable success of cancer immunotherapies. However, clinical responses vary across patients and tumor types. Developing effective cancer therapies and defining critical windows for clinical intervention requires a detailed understanding of the phenotypic and spatiotemporal dynamics of the cell types that make up the tumor microenvironment. Methods To enable high-resolution reconstruction of cell fate decisions in the tumor microenvironment, we developed PEtracer, a prime editing-based lineage tracing system compatible with single-cell sequencing and multimodal imaging, allowing for joint analysis of cell state and lineage in dissociated cells or in intact tissues with high spatial resolution. Results Using PEtracer coupled with single-cell and spatial transcriptomic profiling in syngeneic mouse models of cancer, we reconstructed the growth of individually seeded tumors in vivo, uncovered distinct modules of cell-intrinsic and -extrinsic factors that coordinate tumor growth, and mapped the recruitment and differentiation dynamics of tumor-infiltrating immune cells. Conclusion PEtracer enables high-resolution reconstruction of cell state and lineage dynamics within the tumor microenvironment in vivo. By leveraging prime editing-based lineage recording and multimodal imaging, PEtracer allows systematic dissection of how tumor, immune, and stromal cells evolve during cancer progression and therapeutic response. The resulting spatially resolved multimodal datasets provide a foundation for predictive models of tumor microenvironment dynamics. Funding Source National Institutes of Health Topic Categories Tumor Immunology: Cellular Responses and Tumor Microevironment (TIME)