Spatial epitope barcoding reveals clonal tumor patch behaviors

Intratumoral heterogeneity is a seminal feature of human tumors contributing to tumor progression and response to treatment. Current technologies are still largely unsuitable to accurately track phenotypes and clonal evolution within tumors, especially in response to genetic manipulations. Here, we developed epitopes for imaging using combinatorial tagging (EpicTags), which we coupled to multiplexed ion beam imaging (EpicMIBI) for in situ tracking of barcodes within tissue microenvironments. Using EpicMIBI, we dissected the spatial component of cell lineages and phenotypes in xenograft models of small cell lung cancer. We observed emergent properties from mixed clones leading to the preferential expansion of clonal patches for both neuroendocrine and non-neuroendocrine cancer cell states in these models. In a tumor model harboring a fraction of PTEN-deficient cancer cells, we observed a non-autonomous increase of clonal patch size in PTEN wild-type cancer cells. EpicMIBI facilitates in situ interrogation of cell-intrinsic and cell-extrinsic processes involved in intratumoral heterogeneity. [Display omitted] •EpicTags enable in situ tracking of barcoded cells•EpicMIBI provides spatial, cell-type, and cell-state depiction of clonal tumor patches•Non-neuroendocrine cells display increased local clonal growth•PTEN loss can promote a non-cell autonomous increase of clonal wild-type cell growth Rovira-Clave et al. employ a barcoding system and subcellular multiplex protein imaging to identify clonal behaviors in small cell lung cancer models. Non-neuroendocrine cells display increased local clonal growth compared with neuroendocrine cells. Loss of the PTEN tumor suppressor shifts tumor evolution through cell-intrinsic mechanisms and modifications on neighboring wild-type cells.