The paper introduces SpaceTracer, a new computational framework designed to identify somatic mutations directly from spatial transcriptomics data. By detecting these genetic alterations, the tool allows researchers to perform lineage tracing within the natural architecture of human tissues, bypasssing the need for invasive genetic manipulations. The authors demonstrate that this method can effectively reconstruct the evolutionary history of tumors, revealing how specific cell populations migrate and interact within their environment. Application of the tool to cutaneous squamous cell carcinoma uncovered previously hidden migratory patterns in non-tumor cells and detailed how mutant B cells infiltrate malignant areas. Ultimately, SpaceTracer offers a high-resolution platform for studying tumor-immune ecosystems and complex developmental processes by integrating genomic mutations with spatial gene expression.

References:

• Yang Z, Yao M, Yang Q, et al. Detection of Somatic Point Mutations Directly from Spatial Transcriptomics Enables in vivo Spatiotemporal Lineage Tracing[J]. bioRxiv, 2026: 2026.02. 04.703493.