In early March 2020, when the world turned upside down, we at NanoString told ourselves and our customers “Science doesn’t stop, neither should you” and it turns out our customers were listening!
Indeed, 2020 was a prolific year for scientists who use the nCounter® Analysis System, as they continued to advance scientific research across multiple fields including immuno-oncology, neuroscience, and infectious disease.
At the heart of nCounter Gene Expression Panels are the lists of hundreds of thoroughly vetted and curated genes. Just as important, however, is the flexibility to customize these panels with up to 55 genes with a Panel Plus to tailor the assay to your research project. Below we discuss three examples wherein nCounter panels enabled scientists to make new discoveries.
New therapeutic opportunities for angiosarcoma patients
Human angiosarcomas are rare but highly aggressive soft tissue tumors that affect the inner lining of blood and lymph vessels. A subpopulation of cutaneous head and neck angiosarcomas is characterized by a high tumor mutation burden (TMB) and UV damage mutational signatures. It appears that UV damage may be the driving force behind tumor development. In the publication “Multiomic analysis and immunoprofiling reveal distinct subtypes of human angiosarcoma” [i], the authors sought to better understand the tumor microenvironment and possibly identify targets for checkpoint inhibition immunotherapy. They used the PanCancer IO 360™ Panel to stratify angiosarcoma tumors into three distinct clusters. These three clusters differed in immune cell composition and the level of immune response that further distinguished them into immunologically “hot” or “cold” tumors. Cluster 3 displayed a significant increase in immune cells and inflammatory- and immune-related signaling pathway genes. Cluster 3 tumors had the highest Tumor Inflammation Signature (TIS) scores, a sign that these tumors will likely respond better to immune checkpoint inhibitors. From this detailed analysis, several protein kinases were identified as possible chemotherapeutic targets. Given that the majority of angiosarcoma patients have a grim prognosis, it is important to find new avenues for therapeutic intervention. This novel study was possible because of the curated content and TIS gene signature embedded into the IO 360 Panel.
Alzheimer Disease: There is always more to learn
In the next reviewed publication “A novel systems biology approach to evaluate mouse models of late-onset Alzheimer’s disease” [ii], the authors took advantage of the flexibility of Panel Plus to add 30 custom selected probes to the 770 gene nCounter® Alzheimer’s disease (AD) panel and focused on late-onset Alzheimer’s disease (LOAD). They prioritized 30 human co-expression modules that have a strong association with LOAD and are not significantly divergent between mouse and human. LOAD is the most common form of dementia and because of the difficulties in studying the human progression of this disease, animal models are needed to predict disease progression and identify therapeutic targets. Much of our knowledge about LOAD in humans comes from post-mortem examination of the brain. There are multiple mouse models to study AD pathogenesis; the question asked in this study was which mouse model is most appropriate for preclinical models of LOAD. Three novel mouse models were assessed: APOE4 K1 mice, Trem2*R47H mice, and a cross between these two. These three mouse models carry two human risk variants that are strongly associated with LOAD. Transcriptome analysis of these mice revealed that even when the disease had not progressed to full LOAD pathology, these mice could be successfully used to identify transcriptional disruptions relevant to human disease. Additionally, these mice can be used to dissect the contributions of time and genetic background to LOAD pathogenesis, offering the potential to develop inhibitors for the progression of AD.
Early diagnosis can slow the spread of a contagious disease
Sometimes what a scientist really needs is the option to create a unique own toolkit and the publication “Previremic identification of Ebola or Marburg virus infection using integrated host-transcriptome and viral genome detection”[iii] illustrates this point. Most diagnostic assays look for viral RNA in the blood. In the case of filoviruses like Marburg and Ebola, the virus replicates inside the host organs (such as the spleen and liver), thereby making early detection extremely difficult. Too often the patient is not diagnosed until the virus has replicated enough to accumulate in the circulating blood. Marburg and Ebola are highly infectious and finding a way to detect the virus early is key to preventing deadly outbreaks. The authors of this paper looked for host genes that were upregulated in the course of infection. They found a subset of interferon-stimulated genes (ISGs) that were upregulated in all symptomatic animal data sets. Genes that were upregulated in response to Ebola, hemorrhagic fever, and other viruses were selected for further study using nCounter® Elements™ TagSets. The hope was that these early response biomarkers could flag a potential Ebola infection. Eight of these ISG markers and one Ebola marker were used in an Elements assay to study non-human primates challenged with the Ebola virus. Most animals first showed viremia by Day 5 post infection as determined by a plaque assay. The eight host response genes displayed a clear increase in expression by Day 3 post infection, confirming that host genes can be used for early detection of infection. The team conducted a similar test to identify early infection with Marburg virus and found that, once again, an increased expression in certain host genes preceded the expression of viral markers, enabling early detection of infection 3 days post infection. The flexibility of the Elements TagSets facilitated the creation of a two-step, “sample-to-answer” assay for these highly contagious, deadly viruses. Early detection of pre-symptomatic individuals will be key to identifying and containing viral exposure and this assay is a step in that direction.
 Chan JY, Lim JQ, Yeong J, et al. Multiomic analysis and immunoprofiling reveal distinct subtypes of human angiosarcoma. J Clin Invest. 2020;130(11):5833-5846. doi:10.1172/JCI139080
 Preuss C, Pandey R, Piazza E, et al. A novel systems biology approach to evaluate mouse models of late-onset Alzheimer’s disease. Mol Neurodegener. 2020;15(1):67. Published 2020 Nov 10. doi:10.1186/s13024-020-00412-5
 Speranza E, Caballero I, Honko AN, et al. Previremic Identification of Ebola or Marburg Virus Infection Using Integrated Host-Transcriptome and Viral Genome Detection. mBio. 2020;11(3):e01157-20. Published 2020 Jun 16. doi:10.1128/mBio.01157-20
FOR RESEARCH USE ONLY. Not for use in diagnostic procedures.