Lecture
Single Cell Sequencing of FFPE Samples: Bridging Pathology and Discovery
- at -
- ICM Saal 2
- Type: Lecture
Lecture description
Formalin-fixed, paraffin-embedded (FFPE) tissue archives represent one of the largest and most clinically annotated biological resources available today. However, RNA degradation and chemical modification have greatly limited the application of singlecell RNA sequencing to FFPE samples, restricting transcriptomic analysis largely to bulk or spatially averaged approaches.
Here, we present a novel single-cell RNA analysis technology specifically designed to enable robust whole transcriptome profiling from FFPE-derived single nuclei. By combining optimized nuclei extraction from FFPE samples, random RT priming and subsequent tagging of the cDNA, this approach overcomes key technical barriers associated with single cell analysis in archived samples. The random-priming strategy in RT step enables coverage across gene body and makes mutation detection possible. Furthermore, our method can sequence not only mRNA but also non-coding RNAs with single cell resolution.
We demonstrate the performance of this technology across multiple FFPE tissue types, highlighting reproducibility, sensitivity, and biological interpretability. Importantly, we focus not only on technical metrics, but on the ability to extract actionable biological insights—such as accurate cell-type annotation, disease-relevant expression profiles, and treatment-related cell composition changes—from samples previously considered incompatible with single-cell analysis. The method is automated and suitable for routine testing.
This work expands the scope of single-cell transcriptomics to clinically relevant archived specimens, enabling retrospective studies, translational research, and new connections between molecular phenotypes and long-term clinical outcomes. By bridging the gap between archived pathology samples and single-cell resolution, this technology opens new opportunities for discovery in both research and clinical translational settings.
Here, we present a novel single-cell RNA analysis technology specifically designed to enable robust whole transcriptome profiling from FFPE-derived single nuclei. By combining optimized nuclei extraction from FFPE samples, random RT priming and subsequent tagging of the cDNA, this approach overcomes key technical barriers associated with single cell analysis in archived samples. The random-priming strategy in RT step enables coverage across gene body and makes mutation detection possible. Furthermore, our method can sequence not only mRNA but also non-coding RNAs with single cell resolution.
We demonstrate the performance of this technology across multiple FFPE tissue types, highlighting reproducibility, sensitivity, and biological interpretability. Importantly, we focus not only on technical metrics, but on the ability to extract actionable biological insights—such as accurate cell-type annotation, disease-relevant expression profiles, and treatment-related cell composition changes—from samples previously considered incompatible with single-cell analysis. The method is automated and suitable for routine testing.
This work expands the scope of single-cell transcriptomics to clinically relevant archived specimens, enabling retrospective studies, translational research, and new connections between molecular phenotypes and long-term clinical outcomes. By bridging the gap between archived pathology samples and single-cell resolution, this technology opens new opportunities for discovery in both research and clinical translational settings.
