Decoder-FFPE-seq enables sensitive, genome-wide spatial transcriptomics of archival tissues at single-cell resolution

Formalin-fixed paraffin-embedded (FFPE) tissue-compatible spatial transcriptomics (ST) is transforming biology and histopathology, but achieving high sensitivity, genome-wide coverage, single-cell resolution, and researcher accessibility remains challenging. To address these challenges, we here present a dendrimeric DNA coordinate barcoding design for FFPE tissue-adapted spatial RNA sequencing (Decoder-FFPE-seq) by integrating RNA-to-DNA probe conversion with blotting-assisted barcoding. Decoder-FFPE-seq provides single-cell resolution with a >2.6-fold sensitivity increase in whole-transcriptome mouse brain and archived human sample profiling over existing platforms, resolving potential cellular identity of low-abundance genes, finer tissue architecture, and capturing an epithelial-mesenchymal transition-associated signature for prognostic value. With expanded probe libraries, Decoder-FFPE-seq captures long noncoding and viral RNAs, revealing their spatial coregulatory networks with messenger RNAs in oral squamous cell carcinomas (OSCCs). In an OSCC immunotherapy cohort, two CD8⁺ T cell subpopulations were respectively identified in pre- and postchemoimmunotherapy samples, potentially linked to treatment response. Decoder-FFPE-seq establishes a robust, high-resolution, and accessible framework for sensitive ST profiling of archival tissues in fundamental and translational studies.