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Stereo-seq V2: Spatial mapping of total RNA on FFPE sections with high resolution
1State Key Laboratory of Genome and Multi-omics Technologies, BGI Research, Shenzhen 518083, China.
Cell
|August 29, 2025
Summary
Stereo-seq V2 enables spatial transcriptomics on FFPE samples, improving RNA profiling for cancer research and infectious disease studies. This new method enhances sensitivity and coverage for diverse RNA types.
Area of Science:
- Genomics
- Molecular Biology
- Biotechnology
Background:
- Spatial transcriptomics on formalin-fixed, paraffin-embedded (FFPE) samples is challenging.
- Existing methods struggle with RNA capture and profiling in preserved clinical tissues.
Purpose of the Study:
- Introduce Stereo-seq V2 for high-resolution spatial transcriptomics on FFPE samples.
- Enhance RNA capture efficiency, gene body coverage, and profiling of non-polyadenylation (poly(A)) RNAs.
- Enable simultaneous host and pathogen transcriptome analysis.
Main Methods:
- Utilized random primers for in situ RNA capture and sequencing on FFPE sections.
- Applied Stereo-seq V2 to triple-negative breast cancer (TNBC) FFPE samples.
- Analyzed a Mycobacterium tuberculosis (Mtb)-infected mouse model for host-pathogen gene expression dynamics.
Main Results:
- Achieved single-cell resolution RNA profiling on FFPE sections.
- Demonstrated unbiased transcript capturing and uniform gene body coverage.
- Identified tumor-specific alternative splicing events in TNBC and Mtb-specific BCR clones in infected lungs.
Conclusions:
- Stereo-seq V2 offers robust performance for FFPE sample analysis.
- The technology enhances sensitivity for marker genes and non-polyadenylation (poly(A)) RNA profiling.
- Stereo-seq V2 shows significant potential for biomedical research and personalized medicine.
