What’s New at NanoString for 2023: The Arrival of the First Fully Integrated Single-Cell Spatial Solution

One of the interesting hallmarks of celebrating the start of a new year is the consumption of special foods. For example, in the American South Hoppin’ John, or black-eyed peas, rice, greens, and cornbread is a common dish. Why? Black-eyed peas represent coins, money is green, and cornbread is gold. Therefore, consuming this dish is thought to bring prosperity and good luck in the new year.

Las doce uvas de la suerte, or the twelve grapes of luck, is a tradition started in Spain and celebrated in Latin America, the Philippines and Hispanic communities in the United States. Traditionally, people endeavor to eat twelve grapes when the bell tolls midnight on New Year’s to bring luck and prosperity in all twelve months of the new year. In Germany and Austria, people exchange Glücksschwein, or good luck pigs, with one another. In Japan, people eat buckwheat soba noodles for longevity and prosperity.

What commonality do we see in these traditions spanning across the world? All involve bringing good fortune, and in particular, prosperity into the new year. Although many think of building wealth as a central part of prosperity, it is also synonymous with success. How can the latest spatial biology techniques help you succeed in your research? 

How the Latest Spatial Biology Techniques Can Help your Research Prosper

Spatial Biology was named method of the year by Nature Methods in 2020 for its potential to revolutionize our understanding of molecular tissue architecture. The method uses two common molecular biology techniques in tandem: immunofluorescence and next-generation sequencing. Therefore, spatial biology approaches provide information simultaneously on both transcriptional dynamics and location of gene expression within the cell.

Now scientists can view spatial transcriptomics or transcriptional dynamics within their cellular context. A context that is critically important to fully understanding molecular processes. Previously, techniques such as single-cell analysis could provide very specific information, but without the context. Other approaches provided context, but without specific detail. Spatial biology provides a sweet spot. Researchers see a more complete picture of what is occurring in the tissue that is neither too broad nor too specific.  

Breakthrough Instruments in the World of Spatial Biology

Nanostring unveiled the GeoMx® Digital Spatial Profiler in 2019. The Digital Spatial Profiler (DSP) allows for the researcher to gain a bird’s eye view of gene expression within a particular region. The GeoMx DSP facilitates the analysis of up to 60 samples per week with approximately 30 minutes of hands-on time for researchers. Therefore, GeoMx can serve as a spatial biology insight factory. Since its launch in 2019, more than 375 laboratories adopted GeoMx DSP and more than 175 publications resulted from its use. 

2023 sees the arrival of the next step forward in spatial biology research: the unveiling of the first fully integrated single-cell spatial solution. Just last month, Nanostring shipped its first spatial solution. The first fully integrated single-cell spatial solution consists of the CosMx™ Spatial Molecular Imager and the AtoMx™ Spatial Informatics Platform.

When Cutting-edge Instrumentation Meets AI-powered Analysis

CosMx Spatial Molecular Imager (SMI) provides deeper detail than the GeoMx Digital Spatial Profiler system. Researchers can examine single cells and quantify more than 1,000 RNA and 64 protein targets. Researchers can use a variety of sample types with the CosMx SMI, including everything from formalin-fixed paraffin embedded samples to organoids. Using the system, researchers can examine which cells are present, their location, biomarker expression patterns, and the organization of their unique tissue microenvironment. Applications include cell typing, microenvironment mapping, examination of ligand-receptor interactions, discovery of biomarkers, and analysis of disease states compared to healthy tissues. 

Nanostring developed a streamlined overnight protocol for the preparation of samples for analysis in the CosMx SMI. In situ hybridization probes with attached single-molecular imaging barcodes are added to samples mounted on glass slides. The slides are then assembled into flow cells. These flow cells are then loaded onto the CosMx Spatial Molecular Imager. The imager can accommodate up to four slides at once. Since protein is imaged alongside RNA, researchers can clearly distinguish cellular boundaries. 

But what makes it the first fully integrated solution? As anyone who has ever collected data will tell you, the analysis can often take substantially longer than the initial data collection! Investing in a bioinformatics architecture to support spatial biology research can be resource intensive for individual laboratories. Therefore, Nanostring also launched the AtoMx Spatial Informatics Platform

The user-friendly AtoMx Spatial Informatics Platform (SIP) requires no coding experience to use and provides researchers with a ready to use cloud-based, secure, and scalable storage option for their spatial biology data. The platform facilitates the entire research process, from study design to publication. Users can choose to use a pre-defined analysis pipeline or customize. AtoMx is also compatible with open-source tools developed by bioinformatics researchers or outside artificial intelligence/machine learning analysis algorithms. In addition, the AtoMx Spatial Informatics Platform is compatible with both the GeoMx Digital Spatial Profiler and CosMx Spatial Molecular Imager. 

It should also be noted that GeoMx Digital Spatial Profiler and CosMx Spatial Molecular Imager perform complementary functions. GeoMx Digital Spatial Profiler excels at unbiased biomarker discovery through its whole transcriptome profiling capabilities. CosMx Spatial Molecular Imager facilitates spatial biology at the single-cell and subcellular levels. Therefore, CosMx Spatial Molecular Imager is perfect for mapping cell-types and examining cellular interactions. Both together, combined with the AtoMx Spatial Informatics Platform, open the door to prosperity in 2023! 

Looking Towards a Prosperous 2023 with the Latest in Spatial Genomics

In December 2022, Nanostring shipped its first commercial CosMx Spatial Molecular Imager with AtoMx Spatial Informatics Platform package. As of late 2022, researchers had already booked an additional 100 complete systems. In a new year equipped with novel tools for spatial biology, the stage is set for a prosperous 2023. What new insights into cell and molecular biology will researchers generate in 2023? What good fortune will these insights bring into clinical settings, leading to better treatments and patient outcomes? How will researchers and ultimately society prosper as the result of the utilization of these new technologies? 

As always, it’s an exciting time to be a molecular biologist. The potential for prosperity with the CosMx Spatial Molecular Imager with AtoMx Spatial Informatics Platform is undisputed. Don’t forget to add in your favorite food this New Years for a boost of extra luck before starting your latest spatial biology experiment!

By Melanie Peffer
For research use only. Not for use in diagnostic procedures.