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An Introduction to Spatial Biology and Spatial Profiling

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NanoString on July 28, 2022

What is spatial biology?

Spatial biology is the study of molecules in a two-dimensional or three-dimensional context. Using spatial biology techniques, the users can visualize molecules in their unique contexts within individual cells and tissues. 

Biological systems exist in three-dimensional space. For many biological processes, spatial orientation and positioning to each other is critical for that process to work. For example, during development, patterning of the body, such as the orientation and number of fingers, is driven by gradients of signaling molecules. Aberrations to this spatially important cell signaling can lead to polydactyl or extra digits. 

Although the importance of structural functional relationships through molecular biology and subdisciplines like developmental biology or related disciplines like neuroscience are well known, spatial biology typically refers to a specific technique for looking at spatially resolved transcriptional dynamics. 

Spatial biology may also be called spatial profiling or sequencing, spatial genomics, or spatial transcriptomics. Regardless of the name, the assay relies on two well-established molecular biology techniques, immunofluorescence and next-generation sequencing. Using both technologies together, the user can ascertain how transcriptional dynamics vary within a spatial context. Spatial information can be obtained at various scales, including at the tissue, single cell, and subcellular levels. 

Spatial biology is a promising new field. Consequently, Nature Methods chose spatially resolved transcriptomics as the method of the year in 2020. Researchers have leveraged spatial biology to gain insights into cancer biology in several cancers, including breast and colorectal cancers. Other groups use spatial biology to create a transcriptional atlas of healthy organs. The goal of the spatial organ atlas is to create a reference material that scientists can use to compare diseased tissue to in order to better understand disease processes. 

Why is spatial biology important?

Spatial biology is important because it allows the user to study how molecules interact in a three-dimensional setting. Since the body also exists in three dimensions, spatial biology techniques give a more precise view of molecular processes in cells and tissues. 

A core foundational principle of molecular biology is that form dictates function. When considering the human body and each of its component parts, the three-dimensional organization of each is critical for the function of the body. This applies not only to a gross scale but also at the molecular level. Therefore, in order to fully understand and appreciate physiology requires attention to spatial organization, and in particular, the spatial organization that is relevant to understanding the biology of a system. 

Changes to our biology and/or physiology are driven by gene expression. Cells within the body are in constant contact with one another through paracrine and endocrine manners. Cells can also regulate themselves through autocrine signaling. Through these signals, transcription factors can be turned on or off, causing changes in gene expression and ultimately in the biology of the cell. 

Given the importance of both transcriptional dynamics and the relationship of form to function, naturally, attention to both at the same time (spatial biology) is critically important to fully understand biological processes. Spatial biology techniques allow the user to examine transcriptional dynamics in their specific and unique spatial context. This is important because the spatial context is important for inferring function, understanding why diseases like cancer occur, and understanding what normal healthy cells and/or tissues look like. Using an enhanced understanding of disease processes, we can better design treatments based on our expanded understanding of exactly how biological processes are playing out with the cell. Examination of genes in spatial context provides critical insight needed for interpreting transcriptional dynamics and our overall understanding of cellular biology. 

What is spatial profiling?

Spatial profiling is the combination of two molecular biology techniques, high-plex gene expression analysis, and immunofluorescence. Spatial profiling leverages both technologies to spatially resolve gene expression. For instance, one can use immunofluorescence to identify a region of interest, then collect all expression transcripts in that area. 

When considering how a biological system functions, an important part to consider is the spatial organization of structures. These structures can be part of an organism’s gross anatomy, such as the location of specific organs, tissue architecture, or the relationship of specific subtypes of cells to one other, either within a tissue or as part of a biological process. For example, what is occurring at the interface between cells of the immune system and a pathogen? 

Spatial profiling uses a combination of next-generation sequencing and immunofluorescence microscopy to understand spatially dictated variation in transcriptional dynamics. Spatial profiling is a relatively new technique and may also be called spatial sequencing, spatial biology, or spatially resolved transcriptomics. The latter term is what Nature Methods referred to this technology as when choosing spatial profiling as the method of the year in 2020. 

Regardless of the term used, all of the technologies rely on using two common molecular biology techniques in tandem. Using microscopy, users are able to select a region of interest. Photocleavable tags are released, which can then be collected by the investigator for next-generation sequencing. Therefore, the user can assess differences in transcriptional dynamics within different regions of the same tissue. Users can also use spatial profiling for single-cell imaging within a tissue or to examine the spatial distribution of transcripts within a single cell.  Biologists have used spatial profiling in a variety of settings and for varying purposes. For example, some have examined differences in gene expression in low- and high-grade tumors in colorectal cancer. Other groups are using spatial profiling to create a spatial organ atlas. A spatial organ atlas would serve as a reference for transcripts in their spatial contexts that can be compared to disease states to better understand disease progression. 

Why is spatial profiling important?

Spatial profiling is important because, at the molecular level, form implies function. Understanding how gene expression works in a three-dimensional context is important for a fuller understanding of molecular and cellular biology.

The human body and its component tissues, organs, and cells exist and function in a three-dimensional system. Without proper spatial arrangement of, for example, organs, the body would not be able to function. Therefore, the understanding of spatial relationships and contexts between different component parts is important for the understanding of biology. 

Without the spatial context, the biological meaning can be unclear. For example, let’s draw an example with a small building in a tree. If the context was someone’s backyard, one may infer that the building in the tree is a child’s treehouse. Conversely, if the small building in the tree was found in a wildlife refuge, it could be a wildlife blind for biologists. Or, if the small building was on public hunting lands, it could also be a blind for hunters. The spatial context around the object of interest is necessary for understanding the purpose. 

An important piece of information to take from a biological context is the transcriptional dynamics and how those dynamics may be different depending on location. When we consider measurable biological changes in the cell, these changes are often wrought by changes in gene expression. For instance, signals from cortisol to the glucocorticoid receptor result in the expression of many gene targets controlling everything from circadian rhythms to cell proliferation.  Spatial profiling is, therefore, critically important for understanding transcriptional dynamics within their spatial context. It combines the power of gene transcription to change biology with one of the key principles of molecular biology, that structure drives function. Assessment of gene expression in spatial context is necessary for the interpretation of the biology of the cell. Furthermore, it provides depth and color to our understanding of molecular processes.

For Research Use Only. Not for use in diagnostic procedures.

Post by NanoString