Spatial transcriptomics

Spatial Transcriptomics

Spatial transcriptomics is a biotechnology that enables the spatial analysis of all mRNAs in individual tissue sections. The technology was conceived and developed by Jonas Frisén, Joakim Lundeberg, Patrik Ståhl and their colleagues (Ståhl et al 2016). The key innovation that drove the development of the technology was the ordered attachment of spatially barcoded reverse transcription oligo(dT) primers to the surface of microscope slides.

When a tissue section is attached to one of these slides the barcoded primers bind and capture adjacent mRNAs from the tissue. With the tissue section still attached to the slide, reverse transcription of captured mRNA is initiated and the resulting cDNA incorporates the spatial barcode of the primer. Following mRNA capture and reverse transcription, sequencing libraries are prepared and analyzed with next-generation sequencing. Thanks to the spatial barcode present within each sequence, the sequencing data for each individual mRNA transcript can be mapped back to its point of origin within the tissue section.

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Publications using spatial transcriptomics (as of April 2018)

Stahl, P. L., F. Salmen, S. Vickovic, A. Lundmark, J. F. Navarro, J. Magnusson, S. Giacomello, M. Asp, J. O. Westholm, M. Huss, A. Mollbrink, S. Linnarsson, S. Codeluppi, A. Borg, F. Ponten, P. I. Costea, P. Sahlen, J. Mulder, O. Bergmann, J. Lundeberg, and J. Frisen. "Visualization and Analysis of Gene Expression in Tissue Sections by Spatial Transcriptomics." Science 353, no. 6294 (2016): 78-82. doi:10.1126/science.aaf2403.

Giacomello, Stefania, Fredrik Salmén, Barbara K. Terebieniec, Sanja Vickovic, José Fernandez Navarro, Andrey Alexeyenko, Johan Reimegård, Lauren S. Mckee, Chanaka Mannapperuma, Vincent Bulone, Patrik L. Ståhl, Jens F. Sundström, Nathaniel R. Street, and Joakim Lundeberg. "Spatially Resolved Transcriptome Profiling in Model Plant Species." Nature Plants 3, no. 6 (2017): 17061. doi:10.1038/nplants.2017.61.

Asp, Michaela, Fredrik Salmén, Patrik L. Ståhl, Sanja Vickovic, Ulrika Felldin, Marie Löfling, José Fernandez Navarro, Jonas Maaskola, Maria J. Eriksson, Bengt Persson, Matthias Corbascio, Hans Persson, Cecilia Linde, and Joakim Lundeberg. "Spatial Detection of Fetal Marker Genes Expressed at Low Level in Adult Human Heart Tissue." Scientific Reports 7, no. 1 (2017). doi:10.1038/s41598-017-13462-5.

Moncada, Reuben, Florian Wagner, Marta Chiodin, Joseph C. Devlin, Maayan Baron, Cristina H. Hajdu, Diane Simeone, and Itai Yanai. "Building a Tumor Atlas: Integrating Single-cell RNA-Seq Data with Spatial Transcriptomics in Pancreatic Ductal Adenocarcinoma." 2018. doi:10.1101/254375.

Commercialization

Spatial transcriptomic products are produced and marketed by the company Spatial Transcriptomics.

References

Stahl, P. L., F. Salmen, S. Vickovic, A. Lundmark, J. F. Navarro, J. Magnusson, S. Giacomello, M. Asp, J. O. Westholm, M. Huss, A. Mollbrink, S. Linnarsson, S. Codeluppi, A. Borg, F. Ponten, P. I. Costea, P. Sahlen, J. Mulder, O. Bergmann, J. Lundeberg, and J. Frisen. "Visualization and Analysis of Gene Expression in Tissue Sections by Spatial Transcriptomics." Science 353, no. 6294 (2016): 78-82. doi:10.1126/science.aaf2403.