NanoString's (NSTG) GeoMx Digital Spatial Profiler Reveals Insights into COVID-19 in Two New Nature Publications

March 31, 2021 6:14 AM EDT

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NanoString Technologies, Inc. (NASDAQ: NSTG), a leading provider of life science tools for discovery and translational research, today announced that two peer-reviewed publications using the GeoMx® Digital Spatial Profiler have been published in Nature and Nature Communications. These papers describe the use of Digital Spatial Profiling (DSP) technology to investigate SARS-CoV-2 infection and drive diagnostic, prevention, and treatment strategies.

The GeoMx DSP was used to profile lung tissue collected on autopsy from patients who had succumbed to COVID-19 infection. Researchers used the Cancer Transcriptome Atlas (CTA) plus a spike-in panel to detect additional lung genes and SARS-CoV-2 virus. In total, over 1,800 genes were interrogated as part of the study. This information enabled the researchers to connect bulk RNA sequencing data to the lung tissue's spatial architecture by looking at the distribution and transcriptional activity of cells, providing an important basis for understanding COVID-19 and lung pathology.

The first study, published in Nature Communications and led by Dr. Christopher Mason at Weill Cornell Medicine, was entitled "Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveal unique host responses, viral diversification, and drug interactions." In this study, the GeoMx platform was used to molecularly characterize alveolar lung tissue. The team found spatially-restricted expression of the gene ACE2—which is a SARS-CoV-2 cellular target—and SARS-CoV-2 virus in some of the same regions. From the spatially-resolved expression profiles, they were able to infer the abundance of different immune and non-immune cells and found unique cellular distributions in COVID-19 patients compared to normal control lung samples.

"We were interested in characterizing the diversity of SARS-CoV-2 circulating in the population as well as the diversity of response to infection within a single patient. By using cell-type deconvolution, we were able to measure relative levels of 16 different cell populations from COVID-19 cases and controls using a single slide from each patient," said Dr. Mason, who serves on NanoString’s Scientific Advisory Board and is a paid consultant for the company. "This deep molecular profiling helped us create a more complete picture of how the virus circulates in the body and how it elicits a variable response in infected individuals."

The second study, "The spatial landscape of lung pathology during COVID-19 progression", was published in Nature and was led by Dr. Robert Schwartz, Dr. Alain Borczuk, and Dr. Olivier Elemento at Weill Cornell Medicine. The team found a difference in immune composition between individuals with early (<14 days) versus late (>30 days) mortality after admission to a hospital with COVID-19 symptoms. In "early" patients, immune cells known as neutrophils were seen at rates comparable to other acute respiratory distress syndromes (ARDS). However, with time it appears that a different pattern emerges; namely, increased abundance of macrophages, more inflammation, and wound healing (fibrosis) in patients with late mortality.

"Spatial profiling of the samples allowed us to separately characterize the transcriptional response in the airway, alveolar, and vascular compartments of the lung, and enabled us to see that the early period of severe COVID-19 disease is comprised of inflammatory responses to SARS-CoV-2," said Dr. Schwartz. "We also discovered late COVID-19 might be driven by pathogen-independent mechanisms of an immune response with aberrant resolution."

"These studies demonstrate the value of the GeoMx Digital Spatial Profiler in characterizing the tissue damage induced by SARS-CoV-2 infection," said Sarah Warren, Ph.D., Senior Director of Translational Science at NanoString. "By applying high-plex molecular profiling on the formalin fixed, paraffin embedded (FFPE) tissues that are safe to work with from COVID-19 autopsies, we can understand how the virus is inducing and altering immune response and tissue repair in the patients' lungs."

The GeoMx Digital Spatial Profiler enables researchers to rapidly and quantitatively characterize tissue morphology with a high-throughput, high-plex RNA and protein profiling system that preserves precious samples for future analyses. NanoString and its collaborators have presented DSP data in dozens of abstracts at major scientific meetings, and in more than 40 peer reviewed publications, demonstrating DSP’s utility to address a wide range of biological questions in FFPE and frozen tissues. Interested parties can learn more about DSP by visiting

NanoString launched its Technology Access Program (TAP) for the recently announced single and subcellular Spatial Molecular Imager to complement the existing TAP program for GeoMx. Under the program, customers can submit tissue samples to NanoString to be analyzed using both spatial profiling platforms and receive a complete data package. Researchers interested in participating in NanoString's Technology Access Program should contact the company at

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