Why Spatial Biology?

Laura Tabellini Pierre on April 10, 2021

Spatial Genomics and Spatial Transcriptomics: these terms carry an exciting space odyssey-like feel, even if they are taking place on planet Earth. Even so, the field of spatial biology is by no means less thrilling and pioneering than the outer reaches of space.

Understanding Spatial Biology

Spatial Biology is defined as the study of tissues within their own 2D or 3D context and is the new frontier of molecular biology. In the same way that GPS captures location coordinates within an area to create a map and track you within it, the same principle can be translated to a cellular and molecular level.

Through this technology we can help map the spatial architecture of a cell and how it talks to and interacts with its surroundings. Spatial biology is like being inside a tissue sample at a molecular level. It enables you to see things that are not possible by sequencing or any other technologies out there.

The GeoMx® Digital Spatial Profiler (DSP), makes spatial genomics and spatial transcriptomics possible using software to visualize the spatial architecture and analyze multiple biomarkers of a tissue sample.

Spatial Biology In Practice

Spatial Biology In Practice

An increasing number of scientists are finding spatial biology extremely useful for studying oncology, immune-oncology, neurobiology, and even COVID research. Check out this link on how other scientists are using spatial biology for their research.

Though single cell genomics and microscopic analysis can provide information on genes and protein expression. With spatial discrimination, these technologies have important pitfalls.

  1. Gene analysis on microdissected or dissociated tissues. Gene expression from laser capture microdissection or single cells can be informative. But, the context of interactions with surrounding cells is lost.
  2. In situ hybridization or standard immunofluorescence. These techniques enable detection and localization of nucleic acid sequences or proteins in fixed tissue. But, has severely limited multiplexing capabilities. They also may suffer from quantitation challenges or extreme non-linearities depending on the method of visualization.

GeoMx DSP has solved both issues, with the added value of being enhanced for the hardest and yet most common sample type of all: formalin-fixed paraffin-embedded (FFPE).

Why does Spatial Omics Matter?

Nature Methods has dubbed Spatial Transcriptomics “Method of the year” for 2020, in honor of its explosive popularity and potential for future insight. In the word of Nature Methods staff: “spatially resolved transcriptomics highlights how these technologies have matured and expanded to give biologists exceptional views of the biology of single cells while retaining information on spatial context.”

Why is GeoMx DSP the Spatial Transcriptomics Technology of the Future?

The key breakthrough with the GeoMx DSP is a spatial approach. Resulting in the whole biology world of microscopy being turned upside down. In typical experiments, a scientist adds detection reagents directly to the tissue and read the results out with a microscope. Through NanoString’s innovative approach, detection is done in a much different manner.

First, each affinity reagent molecule binds to its intended target which is linked to a unique DNA sequence with a UV light-cleavable linker.

Next, these are placed on the tissue section(s) of interest, effectively “staining” them invisibly.

Now, the focused UV light from the microscope liberates the indexing oligonucleotides from a region of interest (ROI). These ROIs are defined by the user within the software, and releases them into the liquid above the slide. They are collected via a thin tube and stored in a plate for subsequent quantitation.

This is repeated for each region of interest.

The spatially resolved pools of oligonucleotides are either hybridized to fluorescent barcodes. As a result, this enables the digital counting of up to ~1 million individual targets per ROI. This is done by using the standard NanoString nCounter® analysis system, or quantified by next-generation sequencing (NGS). Where the entire plate can be pooled into a single tube, purified and sequenced. The reads are processed into digital counts and mapped back to each ROI. This generates a map of protein or transcriptional activity within the tissue architecture.

The power of the NanoString approach to Spatial Biology

The field of spatial biology has seen exceptional growth in companies focused on this field. But NanoString has been the pioneer in this area. Our spatial transcriptomics motto is “any target, any region, any sample”. There are an estimated 5 million FFPE slides in countless repositories, each carrying intact morphological and molecular information. Imagine how much knowledge can be obtained by interrogating any region of these tissue samples. For any biological target – biomarkers, pathways, druggable targets. This helps unravel the information hidden within them. All you need is one slide and the GeoMx Digital Spatial Profiler. Welcome to true spatial transcriptomics!

FOR RESEARCH USE ONLY. Not for use in diagnostic procedures.

Post by Laura Tabellini Pierre