Spatial transcriptomics
How to assess cell biology in the context of a tissue
Leveraging spatial transcriptomics with Hyperion systems
High-plex imaging of protein and RNA simultaneously on one section
Spatial transcriptomics is a method enabling high-dimensional investigation of gene transcription in a spatial context. By characterizing expression profiles, spatial transcriptomics is important for analyzing transcriptional patterns and regulation as well as identifying cellular neighborhoods and characteristics contributing to disease.
While single-cell transcriptomics (or scRNA-seq) has become a standard in clinical and translational research, the need to preserve intact and viable cells excludes many cell types and destroys any organizational learnings. Spatial transcriptomics addresses these limitations, providing a comprehensive understanding of cell identity and function relative to neighboring cells.
Spatial transcriptomics
How to assess cell biology in the context of a tissue
Leveraging spatial transcriptomics with Hyperion systems
High-plex imaging of protein and RNA simultaneously on one section
Spatial transcriptomics is a method enabling high-dimensional investigation of gene transcription in a spatial context. By characterizing expression profiles, spatial transcriptomics is important for analyzing transcriptional patterns and regulation as well as identifying cellular neighborhoods and characteristics contributing to disease.
While single-cell transcriptomics (or scRNA-seq) has become a standard in clinical and translational research, the need to preserve intact and viable cells excludes many cell types and destroys any organizational learnings. Spatial transcriptomics addresses these limitations, providing a comprehensive understanding of cell identity and function relative to neighboring cells.
Is it possible to look at RNA and proteins in a spatial context at the same time?
A cutting-edge workflow combines RNAscope™ technology with Imaging Mass Cytometry™ (IMC™) technology to visualize key mRNA and protein markers on the same slide. IMC is a proven tool for the study of complex cellular interactions in a tissue microenvironment, enabling simultaneous assessment of 40-plus protein and mRNA markers at subcellular resolution.
The Hyperion™ and RNAscope workflow enables concurrent imaging of 12 mRNA probes together with 28 or more protein markers.
Using positive control RNA targets, you can confirm RNA quality in serial sections of tissue samples (breast cancer shown here) in order to confidently move forward with performing co-detection. The detected targets shown have few or no available commercial antibodies; utilizing co-detection in IMC allows visualization of cells that express mRNA for these protein targets of interest.
Why use both spatial transcriptomics and spatial proteomics simultaneously?
Transcripts do not always
translate to proteins
Although there is a relationship between mRNA expression and protein expression in a given cell, that relationship can vary considerably because there are many different regulatory controls on whether and when mRNA gets transcribed into protein. There are also lags in time between mRNA expression and their translation to the protein for which they code. Because cells in an FFPE section are snapshots of the cell at the moment of fixation, there can be large variations in the amount of mRNA and the protein for which it codes in the cell at that moment. Imaging only transcripts or only protein gives a partial picture of the state of a cell at a specific point in time.
Protein and RNA:
Greater than the sum of the parts
Imaging the biodistributions of proteins and mRNA simultaneously in the same tissue section provides a better understanding of the state of each cell: The protein expression shows what the cell has already expressed and the mRNA gives a window into what the cell might have expressed in the future. Both spatial transcriptomics and spatial proteomics are important tools in understanding cellular states, generating a more complete picture of cellular contexture.
How it works: A three-step workflow
Although there is a relationship between mRNA expression and protein expression in a given cell, that relationship can vary considerably because there are many different regulatory controls on whether and when mRNA gets transcribed into protein. There are also lags in time between mRNA expression and their translation to the protein for which they code. Because cells in an FFPE section are snapshots of the cell at the moment of fixation, there can be large variations in the amount of mRNA and the protein for which it codes in the cell at that moment. Imaging only transcripts or only protein gives a partial picture of the state of a cell at a specific point in time.
Experiment considerations
For more detailed information on this workflow and how to plan your experiment, read the technical note Co-Detection of RNA and Protein to Explore Tumor-Immune Interactions Utilizing RNAscope With Imaging Mass Cytometry, which provides an overview of the procedure to detect both RNA and protein targets in an FFPE sample using IMC technology.
Visualize key RNA and protein markers in the same samples with spatial multi-omics
Spatial transcriptomics can be used in conjunction with other omics, such as spatial proteomics, to create a more complete picture of cell behavior and response. By combining spatial transcriptomics with spatial proteomics, knowledge of the cell’s transcriptome can improve understanding of cellular function and activation state, and cellular phenotype can be detected using protein targets in the same tissue.
A spatial multi-omic approach that allows for the co-detection of mRNA and protein markers in the same FFPE section offers the capability to gain deeper insights into cellular and functional diversity.
Co-detection of RNA and protein: Taking the complexity out of spatial biology
Hear from Sara Wrobel, PhD, and Roberto Spada, PhD, about an accessible method for performing simulatneous co-detection of RNA and protein for multiplex imaging through a collaboration between Standard BioTools™ and Bio-Techne.
Using spatial transcriptomics with spatial proteomics to understand the mechanism of immune cell infiltration in melanoma
Daniel Schulz, PhD, Senior Scientist at the University of Zurich, and colleagues investigated how chemokines direct immune cell activity in tumors. Read how he determined the underlying molecular mechanisms of cell behavior, providing a greater opportunity for therapeutic development that effectively enhances antitumor activity.
Hyperion systems: Ideal for combined spatial transcriptomic and spatial proteomic imaging
Assay development time: Because IMC technology uses an antibody reagent cocktail, it is simple to mix and match different antibodies without extensive assay validation.
Assay development time: Because IMC technology uses an antibody reagent cocktail, it is simple to mix and match different antibodies without extensive assay validation.
Assay development time: Because IMC technology uses an antibody reagent cocktail, it is simple to mix and match different antibodies without extensive assay validation.
Resources - How scientists use spatial transcriptomics
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