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The expanding vistas of spatial transcriptomics

Nature Biotechnology volume 41, pages 773–782 (2023)Cite this article

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Abstract

The formation and maintenance of tissue integrity requires complex, coordinated activities by thousands of genes and their encoded products. Until recently, transcript levels could only be quantified for a few genes in tissues, but advances in DNA sequencing, oligonucleotide synthesis and fluorescence microscopy have enabled the invention of a suite of spatial transcriptomics technologies capable of measuring the expression of many, or all, genes in situ. These technologies have evolved rapidly in sensitivity, multiplexing and throughput. As such, they have enabled the determination of the cell-type architecture of tissues, the querying of cell–cell interactions and the monitoring of molecular interactions between tissue components. The rapidly evolving spatial genomics landscape will enable generalized high-throughput genomic measurements and perturbations to be performed in the context of tissues. These advances will empower hypothesis generation and biological discovery and bridge the worlds of tissue biology and genomics.

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Fig. 1: Usage of ST in biological experimentation.
Fig. 2: sST methodology and characterization.
Fig. 3: iST methodology and its characterization.
Fig. 4: The future of contextual genomics.

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Acknowledgements

We thank members of the Chen and Macosko laboratories for helpful discussions. This work was supported by NIH grants R01HG010647, UH3CA246632 and R33 CA246455 (to F.C. and E.Z.M.).

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  1. Broad Institute of Harvard and MIT, Cambridge, MA, USA

    Luyi Tian, Fei Chen & Evan Z. Macosko

  2. Harvard Stem Cell and Regenerative Biology, Cambridge, MA, USA

    Fei Chen

  3. Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA

    Evan Z. Macosko

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Tian, L., Chen, F. & Macosko, E.Z. The expanding vistas of spatial transcriptomics. Nat Biotechnol 41, 773–782 (2023). https://doi.org/10.1038/s41587-022-01448-2

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