High-resolution spatial mapping of cell state and lineage dynamics in vivo with PEtracer
Charting the spatiotemporal dynamics of cell fate determination in development and disease is a long-standing objective in biology. Here, we present the design, development, and extensive validation of PEtracer, a prime editing (PE)-based, evolving lineage tracing technology compatible with both single-cell sequencing and multimodal imaging methodologies, created to jointly profile cell state and lineage in dissociated cells or while preserving cellular context in tissues with high spatial resolution. Using PEtracer coupled with MERFISH spatial transcriptomic profiling in a syngeneic mouse model of tumor metastasis, we reconstructed the growth of individually seeded tumors in vivo and uncovered distinct modules of cell-intrinsic and -extrinsic factors that coordinate tumor growth. More generally, PEtracer enables systematic characterization of cell state and lineage relationships in intact tissues over biologically relevant temporal and spatial scales.
Authors
- William E. Allen (ORCID: https://orcid.org/0000-0002-3674-666X)
- Dawei Sun (ORCID: https://orcid.org/0000-0003-1551-4349)
- Nir Yosef (ORCID: https://orcid.org/0000-0001-9004-1225)
- Jonathan S. Weissman (ORCID: https://orcid.org/0000-0003-2445-670X)
- Pu Zheng (ORCID: https://orcid.org/0000-0002-8047-1472)
- William Colgan (ORCID: https://orcid.org/0000-0002-8328-4672)
- Matthew G. Jones (ORCID: https://orcid.org/0000-0002-0363-4493)
- Kathryn E. Yost (ORCID: https://orcid.org/0000-0001-6807-950X)
- Can Ergen (ORCID: https://orcid.org/0000-0002-3096-2927)
- Reuben A. Saunders (ORCID: https://orcid.org/0000-0003-3487-1579)
- Xiaowei Zhuang (ORCID: https://orcid.org/0000-0002-6034-7853)
- Alexandra Schnell (ORCID: https://orcid.org/0000-0003-3442-7750)
- Luke W. Koblan (ORCID: https://orcid.org/0000-0003-2814-4412)
- Dian Yang (ORCID: https://orcid.org/0000-0002-8455-0047)
- Arun Kumar
- J. S. Sandhu (ORCID: https://orcid.org/0009-0009-2493-926X)
Institutions
- Broad Institute (US)
- Howard Hughes Medical Institute (US)
- Harvard University (US)
- Harvard University Press (US)
- Massachusetts General Hospital (US)
- Whitehead Institute for Biomedical Research (US)
- Weizmann Institute of Science (IL)
- Massachusetts Institute of Technology (US)
- Columbia University (US)
- University of California, Berkeley (US)
- Stanford University (US)
Publication Details
- Journal
- Science
- Published
- 2025-07-24
- DOI
- https://doi.org/10.1126/science.adx3800
- Citations
- 12
- Primary Topic
- Single-cell and spatial transcriptomics
- Type
- article
- Field-Weighted Citation Impact
- 9.67