Exploring tissue architecture using spatial transcriptomics

Deciphering the principles and mechanisms by which gene activity orchestrates complex cellular arrangements in multicellular organisms has far-reaching implications for research in the life sciences. Recent technological advances in next-generation sequencing- and imaging-based approaches have estab...

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Bibliographic Details
Published in:	Nature (London) 2021-08, Vol.596 (7871), p.211-220
Main Authors:	Rao, Anjali, Barkley, Dalia, França, Gustavo S, Yanai, Itai
Format:	Article
Language:	eng
Subjects:	Animals Biology Cancer Data Analysis Disease - genetics Gene Expression Profiling - methods Genes Genetic research Genetic transcription Genomes Genomics Humans Hybridization Hypotheses Hypothesis testing Innovations Life sciences Methods Nervous system Neurosciences Next-generation sequencing Organ Specificity - genetics Perturbation Spatial data Technological change Tissues Transcription, Genetic - genetics Transcriptome
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Summary:	Deciphering the principles and mechanisms by which gene activity orchestrates complex cellular arrangements in multicellular organisms has far-reaching implications for research in the life sciences. Recent technological advances in next-generation sequencing- and imaging-based approaches have established the power of spatial transcriptomics to measure expression levels of all or most genes systematically throughout tissue space, and have been adopted to generate biological insights in neuroscience, development and plant biology as well as to investigate a range of disease contexts, including cancer. Similar to datasets made possible by genomic sequencing and population health surveys, the large-scale atlases generated by this technology lend themselves to exploratory data analysis for hypothesis generation. Here we review spatial transcriptomic technologies and describe the repertoire of operations available for paths of analysis of the resulting data. Spatial transcriptomics can also be deployed for hypothesis testing using experimental designs that compare time points or conditions-including genetic or environmental perturbations. Finally, spatial transcriptomic data are naturally amenable to integration with other data modalities, providing an expandable framework for insight into tissue organization.
ISSN:	0028-0836 1476-4687