- Visium Spatial Gene Expression, developed by 10x Genomics, is a powerful spatial transcriptomics platform that enables researchers to analyze gene expression patterns while preserving spatial context within tissue sections. This technology provides a comprehensive view of cellular organization and molecular processes occurring within complex tissues.
- The system works by using specialized slides containing thousands of circular capture spots, each with unique spatial barcodes and oligo-dT sequences. When tissue sections are placed on these slides, messenger RNA (mRNA) molecules from the tissue bind to these capture spots, maintaining their spatial location information. Each capture spot is approximately 55 micrometers in diameter and contains millions of spatially barcoded oligonucleotides that capture mRNA from the tissue directly above it.
- The workflow begins with tissue optimization and sectioning, followed by fixation and permeabilization steps that preserve tissue morphology while allowing access to RNA molecules. The tissue section undergoes H&E staining, enabling researchers to visualize tissue architecture and correlate it with gene expression data. After imaging, the tissue is permeabilized, allowing RNA molecules to bind to the capture spots below. The captured RNA is then converted to cDNA, incorporating both spatial barcodes and unique molecular identifiers (UMIs).
- Data analysis integrates both the high-resolution tissue images and sequencing data to create comprehensive spatial gene expression maps. The platform’s software combines the histological images with transcriptional data, allowing researchers to visualize gene expression patterns in the context of tissue architecture. Advanced analysis tools enable identification of spatial expression patterns, tissue domains, and cellular interactions.
- Key applications include cancer research, where Visium helps understand tumor heterogeneity and the tumor microenvironment. In neuroscience, it enables mapping of gene expression across different brain regions and layers. Developmental biology studies benefit from tracking spatial gene expression changes during tissue formation and organization. The technology is particularly valuable for understanding complex tissues where spatial organization is crucial for function.
- The platform offers several advantages over traditional methods. It provides whole-transcriptome analysis while maintaining spatial context, allowing researchers to discover novel genes and pathways involved in tissue organization. The technology is compatible with fresh-frozen and now FFPE tissue samples, making it suitable for both research and clinical applications. The method requires no prior knowledge of gene targets, enabling unbiased discovery of spatial expression patterns.
- Technical considerations include tissue quality and optimization of permeabilization conditions. The spatial resolution is determined by the capture spot size, which may contain multiple cells depending on tissue type and cellular density. Data analysis requires significant computational resources and expertise to process and interpret the large datasets generated. Integration with other single-cell technologies can provide complementary information at higher resolution.
- Recent developments have expanded the platform’s capabilities. These include protocols for FFPE tissue compatibility, improved sensitivity, and enhanced analysis tools. New applications continue to emerge, such as spatial multi-omics approaches that combine transcriptomics with protein or epigenetic analysis. The technology continues to evolve, offering increasingly detailed insights into tissue biology.
