Spatial Transcriptomics (ST): Context matters
Uncover the "Where" for every "What"
5/24/2022
Haibo Liu
MERFISH
Spatial transcriptomics
• Spatial transcriptomics is a rapidly growing field that promises to
comprehensively characterize tissue organization and architecture at the single-
cell or subcellular resolution.
• The method of the year of 2020 by Nature Methods
Bulk vs. single-cell vs. spatial transcriptomics
Why ST?
• The tissue environment plays a
critical role during development
• defines asymmetric cell fate decisions
and
• instructs cell movement
• Positional information continues to
be crucial at the adult stage
• exerts tissue-specific functions
• maintains tissue homeostasis
• responds to external cues or
perturbations
• Tissue environment is important in
disease, like cancer.
Overview od spatial transcriptomics
technologies
More details about three major ST technologies
Evolution of ST methods
Methods for spatial transcriptomics
(ISC)
(ISH)
(ISS)
Spatial barcoding, aka, in situ capture (ISC)
In situ Hybridization (ISH)
Experimental approaches
ISH variants
ISH outcomes
In situ Hybridization (ISH) and ISS
Strengths and drawbacks
Localized transcripts coloured by specific gene
Sequencing-based
spatial transcriptomic
methods
ISC
Experimental approaches
ISS
ISC: 10x Visium method highlights
10x Visium ST procedures
ISC outcome
An example of 10x Genomics Visium result
https://www.10xgenomics.com/spatial-transcriptomics
In situ capture (ISC)
Strengths and drawbacks
Comparison of ST technologies
ST data analysis
Data analysis: Preprocessing of raw spatial
transcriptomic data
ISH data:
image correction, stitching,
registration, segmentation,
followed by locating and decoding
individual spots that usually
correspond to a single transcript.
Cell type identification and localization
In situ hybridization (ISH):
• High-plex RNA imaging
• Spatial transcriptomics data at single-cell resolution
• Directly used to identify cell types in an analogous
manner to scRNA-seq
• Can be enhanced by integration with scRNA-seq data
In situ capture (ISC):
• non-single-cell spatial transcriptomic data
• Use deconvolution approaches that make use of
external information or through gene
enrichment strategies
Deconvolution of cell types of capture spots
Characterizing spatial patterns of spatial
transcriptomic profiles
Spatial distribution analysis of neighboring cell types spatial coherent expression patterns
Subcellular structure analysis (ISH data only)
ISC-based ST data analysis workflow
Count matrix generation for ISC ST data
(featureCounts)
Understanding how cells
communicate with the tissue
environment
Evolution of ST data analysis tools
Highligh: Integrative exploratory tools for
spatial data analysis and visualization
Seurat tutorial:
https://satijalab.org/seurat/articles/spatial_vignette.html
https://github.com/drieslab/awesome-spatial-data-analysis
References
• Asp M, Bergenstråhle J, Lundeberg J. Spatially Resolved Transcriptomes-Next Generation Tools for Tissue
Exploration. Bioessays. 2020 Oct;42(10):e1900221. doi: 10.1002/bies.201900221.
• Piñeiro AJ, Houser AE, Ji AL. Research Techniques Made Simple: Spatial Transcriptomics. J Invest Dermatol.
2022 Apr;142(4):993-1001.e1. doi: 10.1016/j.jid.2021.12.014.
• Zhang L, Chen D, Song D, Liu X, Zhang Y, Xu X, Wang X. Clinical and translational values of spatial
transcriptomics. Signal Transduct Target Ther. 2022 Apr 1;7(1):111. doi: 10.1038/s41392-022-00960-w.
• Dries R, Chen J, Del Rossi N, Khan MM, Sistig A, Yuan GC. Advances in spatial transcriptomic data analysis.
Genome Res. 2021 Oct;31(10):1706-1718. doi: 10.1101/gr.275224.121.
• Liu B, Li Y, Zhang L. Analysis and Visualization of Spatial Transcriptomic Data. Front Genet. 2022 Jan
27;12:785290. doi: 10.3389/fgene.2021.785290.
• Lewis SM, Asselin-Labat ML, Nguyen Q, Berthelet J, Tan X, Wimmer VC, Merino D, Rogers KL, Naik SH. Spatial
omics and multiplexed imaging to explore cancer biology. Nat Methods. 2021 Sep;18(9):997-1012. doi:
10.1038/s41592-021-01203-6.
• Longo SK, Guo MG, Ji AL, Khavari PA. Integrating single-cell and spatial transcriptomics to elucidate
intercellular tissue dynamics. Nat Rev Genet. 2021 Oct;22(10):627-644. doi: 10.1038/s41576-021-00370-8.
