Spatial Biology

Technologies in next gen sequencing, tissue imaging, and RNA analysis have given rise to the frontier of spatial transcriptomics, a powerful technique for studying gene expression in the context of heterogeneous cells and tissue architechture. Spatial locations of distinct cell subpopulations can directly influence their functions. Such context is not adequately represented by sequencing techniques alone. Spatial genomic and transcriptomic techniques measure expression levels of all or most genes systematically throughout tissue space, giving important insights into any tissue organization, differentiation, and localization. The technique can be broadly grouped into two approaches: imaging-based or sequencing-based.

Imaging-Based Approach

Imaging-based approaches include situ hybridization-based methods, where imaging probes sequentially hybridized in the tissue, as well as in situ sequencing-based methods, where transcripts are amplified and sequenced in the tissue. In situ hybridization applications detect specific RNA transcripts via hybridization of complementary fluorescent probes.

Sequencing-Based Approach

A limitation of probe-based methods is the requirement of a priori knowledge of gene targets. NGS approaches are thus less biased, as they seek to globally read all polyadenylated mRNA molecules. These methods build on single-cell RNA-Seq technology with the incorporation of barcodes to account for spatial position prior to library preparation. Spatially-barcoded RNAs are then processed for sequencing, where the barcode of each read is used to map the position, while the rest of the sequencing read is mapped to the genome to identify the transcript gene.