From whole-mount to single-cell spatial assessment of gene expression in 3D

Unravelling spatio-temporal patterns of gene expression is crucial to understanding core biological principles from embryogenesis to disease. Monash University researchers review emerging technologies, providing automated, high-throughput, spatially resolved quantitative gene expression data. Novel techniques expand on current benchmark protocols, expediting their incorporation into ongoing research. These approaches digitally reconstruct patterns of embryonic expression in three dimensions, and have successfully identified novel domains of expression, cell types, and tissue features. Such technologies pave the way for unbiased and exhaustive recapitulation of gene expression levels in spatial and quantitative terms, promoting understanding of the molecular origin of developmental defects, and improving medical diagnostics.

Principles of current methods for capturing spatial gene expression


Schematic overview of methods based on imaging profiling of the entire specimen. a In situ hybridisation/fluorescence staining where bound oligonucleotide probes reveal spatial expression via fluorescent dyes. b Digital Spatial Profiling where digital barcodes tag bound oligonucleotides and allow multiplexed spatial profiling. c DNA microscopy where chemical DNA reactions permit spatial imaging. d seqFISH+ where accurate fluorescent barcoding is performed sequentially to improve throughput and generate spatial atlases in situ. e DistMap where Drop-seq technology integrates scRNA-seq data and ISH imaging to reveal spatial gene expression. f STARmap where genes are sequenced in situ using padlock amplification. g Tomo-seq where cryogenic tissue sections are individually analysed by bulk RNA-seq and spatial data triangulated in three axes. h Geo-seq where cryogenic tissue samples are obtained through laser capture microdissection and analysed through bulk RNA-seq with results spatially mapped. i High-definition spatial transcriptomics where cDNA synthesis is performed in situ and spatially barcoded prior to RNA-seq. j Slide-seq where mRNA is barcoded in situ and spatially indexed by SOLiD. k novoSpaRc where scRNA-seq is digitally profiled to virtually reconstruct the tissue. l NASC-seq where 4sU labelling identifies temporal and spatial features of single-cell data. Single-cell RNA-seq (scRNA-seq), in situ hybridisation (ISH), sequencing by oligonucleotide ligation and detection (SOLiD).

Waylen LN, Nim HT, Martelotto LG, Ramialison Ml. (2020) From whole-mount to single-cell spatial assessment of gene expression in 3D. Commun Biol 3, 602. [article]

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