Nature Biotechnology, Published online: 22 July 2026; doi:10.1038/s41587-026-03203-3

The cell-by-cell interactions between neoantigen-expressing tumor cells and tumor-specific T cells remained largely unexplored. A single-cell spatial transcriptomics framework enables mapping of neoantigen-expressing tumor cells and tumor-infiltrating T cells, as well as T cell receptor sequencing. This approach reveals distinct immune niches in the tumor microenvironment and their properties that determine tumor-specific responses.