Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

Patrik L. Ståhl; Fredrik Salmén; Sanja Vickovic; Anna Lundmark; José Fernández Navarro; Jens Magnusson; Stefania Giacomello; Michaela Asp; Jakub O. Westholm; Mikael Huss; Annelie Mollbrink; Sten Linnarsson; Simone Codeluppi; Åke Borg; Fredrik Pontén; Paul Igor Costea; Pelin Sahlén; Jan Mulder; Olaf Bergmann; Joakim Lundeberg; Jonas Frisén

doi:10.1126/science.aaf2403

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

Patrik L. Ståhl, Fredrik Salmén, Sanja Vickovic, Anna Lundmark, José Fernández Navarro, Jens Magnusson, Stefania Giacomello, Michaela Asp, Jakub O. Westholm, Mikael Huss, Annelie Mollbrink, Sten Linnarsson, Simone Codeluppi, Åke Borg, Fredrik Pontén, Paul Igor Costea, Pelin Sahlén, Jan Mulder, Olaf Bergmann, Joakim LundebergJonas Frisén

Breastcancer-genetics

Research output: Contribution to journal › Review article › peer-review

Abstract

Analysis of the pattern of proteins or messenger RNAs (mRNAs) in histological tissue sections is a cornerstone in biomedical research and diagnostics.This typically involves the visualization of a few proteins or expressed genes at a time. We have devised a strategy, which we call "spatial transcriptomics," that allows visualization and quantitative analysis of the transcriptome with spatial resolution in individual tissue sections. By positioning histological sections on arrayed reverse transcription primers with unique positional barcodes, we demonstrate high-quality RNA-sequencing data with maintained two-dimensional positional information from the mouse brain and human breast cancer. Spatial transcriptomics provides quantitative gene expression data and visualization of the distribution of mRNAs within tissue sections and enables novel types of bioinformatics analyses, valuable in research and diagnostics.

Original language	English
Pages (from-to)	78-82
Number of pages	5
Journal	Science
Volume	353
Issue number	6294
DOIs	https://doi.org/10.1126/science.aaf2403
Publication status	Published - 2016 Jul 1

Subject classification (UKÄ)

Medical Genetics and Genomics (including Gene Therapy)

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1126/science.aaf2403

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Ståhl, P. L., Salmén, F., Vickovic, S., Lundmark, A., Navarro, J. F., Magnusson, J., Giacomello, S., Asp, M., Westholm, J. O., Huss, M., Mollbrink, A., Linnarsson, S., Codeluppi, S., Borg, Å., Pontén, F., Costea, P. I., Sahlén, P., Mulder, J., Bergmann, O., ... Frisén, J. (2016). Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. Science, 353(6294), 78-82. https://doi.org/10.1126/science.aaf2403

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title = "Visualization and analysis of gene expression in tissue sections by spatial transcriptomics",

abstract = "Analysis of the pattern of proteins or messenger RNAs (mRNAs) in histological tissue sections is a cornerstone in biomedical research and diagnostics.This typically involves the visualization of a few proteins or expressed genes at a time. We have devised a strategy, which we call {"}spatial transcriptomics,{"} that allows visualization and quantitative analysis of the transcriptome with spatial resolution in individual tissue sections. By positioning histological sections on arrayed reverse transcription primers with unique positional barcodes, we demonstrate high-quality RNA-sequencing data with maintained two-dimensional positional information from the mouse brain and human breast cancer. Spatial transcriptomics provides quantitative gene expression data and visualization of the distribution of mRNAs within tissue sections and enables novel types of bioinformatics analyses, valuable in research and diagnostics.",

author = "St{\aa}hl, {Patrik L.} and Fredrik Salm{\'e}n and Sanja Vickovic and Anna Lundmark and Navarro, {Jos{\'e} Fern{\'a}ndez} and Jens Magnusson and Stefania Giacomello and Michaela Asp and Westholm, {Jakub O.} and Mikael Huss and Annelie Mollbrink and Sten Linnarsson and Simone Codeluppi and {\AA}ke Borg and Fredrik Pont{\'e}n and Costea, {Paul Igor} and Pelin Sahl{\'e}n and Jan Mulder and Olaf Bergmann and Joakim Lundeberg and Jonas Fris{\'e}n",

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doi = "10.1126/science.aaf2403",

language = "English",

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Ståhl, PL, Salmén, F, Vickovic, S, Lundmark, A, Navarro, JF, Magnusson, J, Giacomello, S, Asp, M, Westholm, JO, Huss, M, Mollbrink, A, Linnarsson, S, Codeluppi, S, Borg, Å, Pontén, F, Costea, PI, Sahlén, P, Mulder, J, Bergmann, O, Lundeberg, J & Frisén, J 2016, 'Visualization and analysis of gene expression in tissue sections by spatial transcriptomics', Science, vol. 353, no. 6294, pp. 78-82. https://doi.org/10.1126/science.aaf2403

TY - JOUR

T1 - Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

AU - Ståhl, Patrik L.

AU - Salmén, Fredrik

AU - Vickovic, Sanja

AU - Lundmark, Anna

AU - Navarro, José Fernández

AU - Magnusson, Jens

AU - Giacomello, Stefania

AU - Asp, Michaela

AU - Westholm, Jakub O.

AU - Huss, Mikael

AU - Mollbrink, Annelie

AU - Linnarsson, Sten

AU - Codeluppi, Simone

AU - Borg, Åke

AU - Pontén, Fredrik

AU - Costea, Paul Igor

AU - Sahlén, Pelin

AU - Mulder, Jan

AU - Bergmann, Olaf

AU - Lundeberg, Joakim

AU - Frisén, Jonas

PY - 2016/7/1

Y1 - 2016/7/1

N2 - Analysis of the pattern of proteins or messenger RNAs (mRNAs) in histological tissue sections is a cornerstone in biomedical research and diagnostics.This typically involves the visualization of a few proteins or expressed genes at a time. We have devised a strategy, which we call "spatial transcriptomics," that allows visualization and quantitative analysis of the transcriptome with spatial resolution in individual tissue sections. By positioning histological sections on arrayed reverse transcription primers with unique positional barcodes, we demonstrate high-quality RNA-sequencing data with maintained two-dimensional positional information from the mouse brain and human breast cancer. Spatial transcriptomics provides quantitative gene expression data and visualization of the distribution of mRNAs within tissue sections and enables novel types of bioinformatics analyses, valuable in research and diagnostics.

AB - Analysis of the pattern of proteins or messenger RNAs (mRNAs) in histological tissue sections is a cornerstone in biomedical research and diagnostics.This typically involves the visualization of a few proteins or expressed genes at a time. We have devised a strategy, which we call "spatial transcriptomics," that allows visualization and quantitative analysis of the transcriptome with spatial resolution in individual tissue sections. By positioning histological sections on arrayed reverse transcription primers with unique positional barcodes, we demonstrate high-quality RNA-sequencing data with maintained two-dimensional positional information from the mouse brain and human breast cancer. Spatial transcriptomics provides quantitative gene expression data and visualization of the distribution of mRNAs within tissue sections and enables novel types of bioinformatics analyses, valuable in research and diagnostics.

UR - http://www.scopus.com/inward/record.url?scp=84976875145&partnerID=8YFLogxK

U2 - 10.1126/science.aaf2403

DO - 10.1126/science.aaf2403

M3 - Review article

C2 - 27365449

AN - SCOPUS:84976875145

SN - 0036-8075

VL - 353

SP - 78

EP - 82

JO - Science

JF - Science

IS - 6294

ER -

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

Abstract

Subject classification (UKÄ)

UN SDGs

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Multidimensional transcriptomics provides detailed information about immune cell distribution an identity in HER2+ breast tumors

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