Spatial transcriptomics
Methods that read which genes are switched on in each spot or cell of a tumour slice while keeping the tissue's geography, so scientists can see how cancer, immune and stromal cells sit next to one another.
Overview
Spatial transcriptomics measures gene expression across a tissue section without losing position. Sequencing-based platforms capture RNA on barcoded spots (10x Genomics Visium), while imaging-based platforms read hundreds to thousands of RNA species in place at single-cell resolution (MERFISH, 10x Xenium, NanoString CosMx). In oncology it maps the tumour microenvironment, immune exclusion and clonal territories, and it underpins atlases such as the Human Tumor Atlas Network.
How it works
Tissue sections are either overlaid on barcoded capture arrays whose oligonucleotides record position before sequencing, or hybridised with fluorescent probes read out over many imaging rounds with combinatorial barcodes.
- Keeps position, which single-cell sequencing discards
- Reveals immune exclusion, niches and cell neighbourhoods
- Works on archived formalin-fixed tissue on newer platforms
- Costly and data-heavy, mostly research use
- Spot-based methods mix several cells per spot
- No agreed clinical assay yet
Latest papers
topQuery for this technology: (TITLE:"Spatial transcriptomics" OR ABSTRACT:"Spatial transcriptomics") AND (cancer OR tumor OR tumour OR oncology OR carcinoma OR lymphoma OR leukemia OR leukaemia OR myeloma OR sarcoma OR melanoma OR glioma). Results are unfiltered search hits about Spatial transcriptomics, not a curated reading list.
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