Abstract
Innovation in genomics, transcriptomics, and proteomics research has created a plethora of state-of-the-art techniques such as nucleic acid sequencing and mass-spectrometry-based proteomics with paramount impact in the life sciences. While current approaches yield quantitative abundance analysis of biomolecules on an almost routine basis, coupling this high content to spatial information in a single cell and tissue context is challenging. Here, current implementations of spatial omics are discussed and recent developments in the field of DNA-barcoded fluorescence microscopy are reviewed. Light is shed on the potential of DNA-based imaging techniques to provide a comprehensive toolbox for spatial genomics and transcriptomics and discuss current challenges, which need to be overcome on the way to spatial proteomics using high-resolution fluorescence microscopy.
Highlights
Genomics and transcriptomics research techniques can be subdivided into de created a plethora of state-of-the-art techniques such as nucleic acid novo – for example, sequencing-based sequencing and mass-spectrometry-based proteomics with paramount impact in the life sciences
Light is shed on the potential of DNA-based imaging techniques to provide a comprehensive toolbox for spatial genomics and transcriptomics and discuss current challenges, which need to be overcome on the way to spatial proteomics using high-resolution fluorescence microscopy
In an ideal scenario, where fluorescence microscopy would become the prime tool for spatial omics, its resolution should be improved to the size of single proteins (e.g., 5 nm or better spatial resolution), multiplexing capabilities be enhanced to hundreds or even thousands of target species, and small efficient high-performance labeling reagents be developed
Summary
While technical approaches described above provide exquisite high-content information, they struggle to obtain spatial information. In an ideal scenario, where fluorescence microscopy would become the prime tool for spatial omics, its resolution should be improved to the size of single proteins (e.g., 5 nm or better spatial resolution), multiplexing capabilities be enhanced to hundreds or even thousands of target species, and small efficient high-performance labeling reagents be developed. We here focus on different strategies for DNA, RNA, and protein multiplexing using DNA-based labeling probes These approaches can further be combined with state-ofthe-art super-resolution modalities,[12,13,14,15] technically approaching spatial resolutions of better than 5 nm.[16,17,18]. There have been efforts to automate[23] sequential multiplexed super-resolution microscopy in order to routinely achieve >10 target multiplexing
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