Placing RNA in context and space – methods for spatially resolved transcriptomics

Abstract

Single-cell transcriptomics provides us with completely new insights into the molecular diversity of different cell types and the different states they can adopt. The technique generates inventories of cells that constitute the building blocks of multicellular organisms. However, since the method requires isolation of discrete cells, information about the original location within tissue is lost. Therefore, it is not possible to draw detailed cellular maps of tissue architecture and their positioning in relation to other cells. In order to better understand the cellular and tissue function of multicellular organisms, we need to map the cells within their physiological, morphological, and anatomical context and space. In this review, we will summarize and compare the different methods of in situ RNA analysis and the most recent developments leading to more comprehensive and highly multiplexed spatially resolved transcriptomic approaches. We will discuss their highlights and advantages as well as their limitations and challenges and give an outlook on promising future applications and directions both within basic research as well as clinical integration.

Personalized medicine—concepts, technologies, and applications in inflammatory skin diseases

“…Just as for DNA sequencing, single-cell RNA-sequencing (scRNA-seq) is now opening a window to the cellular phenotype, as it allows for unprecedented detail analysis of cellular heterogeneity and development (62,63). Finally, novel in situ sequencing techniques such as fluorescent in situ sequencing of RNA (FISSEQ) (64) and STARmap (65) allow for determination of the actual, 3-dimensional location of gene expression in cells and tissues (66).…”

“…The interpretation of such studies, however, can be difficult, in particular if the starting material contains a mixture of different cell types, each with their own, highly cell-type specific epigenome. Thus, it is necessary to perform cell-type specific deconvolution of the signal in order to identify relevant epigenetic changes rather than just a shift in proportion of cell types (66,68). 8 For studying the 'histone code', genome-wide histone modification assays apply chromatin immunoprecipitation (ChIP) and histone modification-specific antibodies (to precipitate the DNA-histone complexes), followed by NGS (ChIP-seq) to identify the bound DNA fragments.…”

Evaluation of direct grafting strategies in Expansion Microscopy

“…In turn, this allows the use of signal amplification approaches in expansion microscopy, and the study of low-abundance species with high signal-to-noise ratios relative to standard approaches. Again, sequential or combined/orthogonal coupling of the multivalent linker to oligo tiling probes with hybridization chain reaction initiator sequence (HCR) [15][16][17][18] or amplification primers (RollFISH) [19][20][21] allows the creation of multifunctional ISH probe sets, in only a few hours and from commercial oligonucleotides. To demonstrate this, we conjugated tiling probe libraries to the smHCR initiator probes, all coupled through multifunctional linkers (Figure 4, panel a).…”

A compendium on single‐cell analysis for the curious

“…The review ‘Placing RNA in context and space – methods for spatially resolved transcriptomics’ by Strell et al . provides a comprehensive overview of advantages and disadvantages of the current in situ RNA analysis technologies and provides an outlook on the future uses of these technologies in routine diagnostics. In the review entitled ‘Expansion microscopy: enabling single‐cell analysis in intact biological systems’, Alon et al .…”

“…However, new approaches are also emerging for highly parallel protein [8] and epigenetic spatial detection methods [9]. The review 'Placing RNA in context and spacemethods for spatially resolved transcriptomics' by Strell et al [10] provides a comprehensive overview of advantages and disadvantages of the current in situ RNA analysis technologies and provides an outlook on the future uses of these technologies in routine diagnostics. In the review entitled 'Expansion microscopy: enabling single-cell analysis in intact biological systems', Alon et al [11] summarize the state-of-the-art in expansion microscopy techniques as a means to improve spatial resolution.…”