NanoString-based publications 2018: A year in review
2018 was an incredibly productive year for scientific publications showcasing the NanoString platform and assays. We added nearly 500 publications of various scientific disciplines which are available on our website here. Below are some of the highlights of the year.
It’s become clear over the last few years that a key area of biomedical research is to understand the role of the immune system in the development of disease. The discipline of immunology traverses multiple areas of science from infectious disease and vaccines to the management and treatment of chronic diseases such as autoimmune disorders and cancer. However, it is also becoming clear that immune responses are key to the development of many common disorders not traditionally viewed as immunological, including metabolic, cardiovascular, and neurodegenerative conditions. To that end, our first paper of the year on January 1st,2018, adopted a NanoString multiplexed assay to understand potential biomarkers involved in the metabolic issues of maternal obesity and excessive gestational weight gain by utilizing a custom CodeSet representing targets involved in the immune response, inflammation, angiogenesis and growth.
This aspect of the immune response to disease became a central theme for many 2018 publications, especially when embracing some of our fundamental off-the-shelf gene expression panels (PanCancer Immune Profiling, Myeloid, Immunology, Inflammation and our new IO 360™ and Autoimmunity collection). Many of these Immunology-focused panels were utilized for uncovering gene signatures associated with novel treatment options for various tumor types. Among some of the publications in this area the use of a genetically engineered vaccinia virus (VACV) has emerged as an attractive agent especially when exploited as an oncolytic virus coupled to immune checkpoint blockade. While reviewed comprehensively in many articles, the generation of these genetically engineered oncolytic viruses now affords a safer and more efficacious treatment, including arming VACVs with cytokines and immuno-stimulatory molecules and anti-angiogenic agents in addition to combining VACVs with conventional radiotherapy, chemotherapy and immunotherapy. Two articles published in December combined the use of VCAV to either MAPK inhibition or Immunotherapy, with both articles using mouse models of various tumor types coupled to a gene expression readout with the PanCancer Immune Profiling Panel.
2018 also marked our first IO360™ Panel publication. This unique panel offers a 360-degree view of gene expression for the tumor, microenvironment and immune response to quickly evaluate immune evasion and develop potentially predictive signatures. The 770-gene multiplex panel contains 47 potentially predictive biological signatures including the 18-gene Tumor Inflammation Signature*. While it is well established that immune checkpoint blockade (especially for CTLA4 and PD1 pathways) has emerged as a critical treatment against various cancer types we still have a limited understanding of how immune checkpoint blockers engage the complex tumor microenvironments and which mechanisms define treatment success during the time when tumor rejection occurs. The goal of this recent paper was to track key readouts of immunotherapy function during tumor rejection and decipher how immune-mediated tumor control is achieved with a combination of approaches that included the comprehensive IO360 gene expression profiling. The role and interactions between the tumor and its microenvironment is featured in many of our publications, not least in establishing that the tumor microenvironment can also influence disease prognosis and is also likely to be considered as an important prognostic factor. In addition, many of these publications underscore that conventional therapies can influence the microenvironment and antitumor immunity and similarly the TME will influence the effectiveness of therapy (examples include this paper and this).
Our new GeoMx™ Digital Spatial Profiler allows the selection of the different components of each tumor under microscopic control coupled to a panel of markers. It enables dissection of the microenvironment from the tumor environment as well as investigating the heterogeneity of the tumor. Two back-to-back articles were published in the esteemed journal Nature Medicine which feature data collected via the Technology Access Program using the GeoMx platform. In these articles, investigators at the Netherlands Cancer Institute led by Dr. Christian Blank and at the MD Anderson Cancer Center led by Dr. Jennifer Wargo, report data from parallel but independent clinical trials to explore the efficacy of anti-PD-1 and/or anti-CLTA4 combination immunotherapy plus surgery in patients with early stage melanoma. The goal of these studies was to assess safety of the treatment regimen and look for evidence of immune activity in response to treatment. Because of the GeoMx profiling, they discovered markers of antigen presentation (β2M) and T cells (CD3) present on pretreatment tumor biopsies correlated with clinical efficacy in both studies. Clinically, the responses to therapy were strong enough to merit larger trials and continued investigation of the most effective way to leverage immunotherapy.
In 2018 we launched our Autoimmunity Panel collection. While not yet published, we have witnessed this arena of research addressing biomarker insight into type-1 diabetes, allergy, systemic lupus erythematosus and colitis from customers adopting the use of other immunology panels or a custom codeset (examples: 1, 2 and 3).
The immune response has also featured heavily in the field of Neuroscience and this has led to an advancement in our understanding of how immune cells survey the CNS and periphery for the presence of pathogens and tissue damage or degeneration- a common pathology associated with Parkinson’s or Alzheimer’s. Microglia cells are central to this CNS immune surveillance and to the establishment and protection of CNS integrity. Many articles using NanoString custom codesets presented how the roles played by microglia and the immune system change with the maturing CNS, from the active shaping of developing neuronal networks during embryogenesis to surveillance for degeneration and resolution of damage in adulthood (see here, here, and here). Late in 2017, we launched our Neuroscience Panels focused on Neuropathology and Neuroinflammation. Many of our customers have adopted their use, but our first article featuring the Neuropathology Panel (together with the PanCancer Progression and Immune Profiling panels) was recently published for a study investigating novel approaches to the management of Glioblastoma (GBM). The group were interested in identifying pathways critical for GBM initiating cell function as well as developing new strategies that could target these initiating cells to potentially improve GBM patient survival.
Beyond immune associations, neuro-focused aspects of addiction and psychiatric disorders have also featured heavily in NanoString publications bringing with it a better understanding of these highly complex behaviors. One of the major gaps in our current knowledge is understanding how altered function of individual nerve cells can subsequently lead to abnormalities in complex behavior. Such an understanding requires a more sophisticated comprehension of brain function at a neural circuit level but use of gene expression assays such as NanoString have allowed that potential to be realized. With what I describe as having one of the best attention-grabbing titles in research published in the journal Science, groups from Sweden and the US sought to identify molecular mechanisms of addiction and what mediates compulsive alcohol drinking at the expense of other high-value options (https://www.ncbi.nlm.nih.gov/pubmed/29930131). Application of a custom NanoString assay that contained probes targeting 310 transcripts previously hypothesized to be involved in drug addiction demonstrated that impaired GABA clearance within the amygdala contributes to alcohol addiction, appears to translate between species, and may offer targets for new pharmacotherapies for treating this disorder and perhaps other addictive behaviors.
While all the biology textbooks from my college days would indicate that RNA was only represented by mRNA, tRNA and rRNA, we’ve certainly learnt to appreciate the existence of other regulatory RNA molecules. One of the most published panels from NanoString is the miRNA panel. The miRNAs included in either the human, mouse, or rat panels account for 95% of the observed signaling reads in the miRbase repository. In addition, confidence levels, observed ratios, and expression analytics are provided to ensure that the content is weighted towards biologically relevant miRNAs that are actionable and clinically relevant. These panels are ideally suited for targeted discovery and validation experiments and have been published with a variety of samples including FFPE, fresh frozen, cell lines, biofluids such as plasma, urine and serum and exosomes and other extracellular vesicles (example 1, example 2, example 3, example 4).
Other non-coding RNAs include circular RNAs (circRNAs), but unlike linear RNAs, they form covalently closed continuous loops and act as gene regulators in mammals. They were originally thought to represent errors in splicing and considered to be of low abundance, however, there is now an increased appreciation of their important function in gene regulation. Working with our bioinformatics team, a group in Denmark wished to explore the landscape of circRNA expression in B-cell malignancies, particularly since other methods for their quantification have several limitations preventing their development in clinically applicable assays. The group designed NanoString custom assays for simultaneously analyzing 52 unique circRNAs in cell lines and paired fresh frozen and formalin-fixed, paraffin-embedded (FFPE) patient samples (including mantle cell lymphoma, multiple myeloma, follicular lymphoma, diffuse large B-cell lymphoma, Burkitt lymphoma and chronic lymphocytic leukemia). The data obtained were compared to RNA-seq and reverse transcription-qPCR (RT-qPCR) data obtained on the same samples. Importantly, the NanoString circRNA expression profiles were able to distinguish different B-cell malignancies.
I wrap up this blog with our last publication of the year bringing us back to uncovering the role of immune responses through NanoString assays. Aspergillus fumigatus (A. fumigatus) is a wide-spread fungus that is a potent allergen in hypersensitive individuals but also an opportunistic pathogen in immuno-compromised patients. The aim of the study was to analyze primary human bronchial epithelial cells (HBECs) grown at the air-liquid interface (ALI) to determine their transcriptomic and proteomic responses following interaction with A. fumigatus conidia. 2018 saw an overall increase in publications using nuanced methodologies involving both rRNA and mRNA for pathogen detection that included not just multiplexed assays but also multi-species assays (such as this, this, and this).
There are of course many other exciting areas of research that have utilized NanoString that, unfortunately, I didn’t have the opportunity to summarize, but I would encourage readers to look through our regularly updated publications webpage. While 2018 demonstrated adoption of NanoString assays in the scientific community, I have no doubt that 2019 and beyond will reveal even more important discoveries using our technology. Keep up the good science work, everyone!
*Ayers, Mark, et al. “IFN-y-related mRNA profile predicts clinical response to PD-1 blockade.” The Journal of Clinical Investigation 127.8 (2017).