How nCounter helps vaccine research: Part 1, Improving Vaccines

Melanie Peffer on September 27, 2021

I really dislike needles. In fact, I’m downright needle-phobic

When I was notified of my eligibility to receive my COVID-19 vaccine, it was without a doubt the most excited I had ever been to schedule an appointment for a poke. 

Now, I’m not the only one who dislikes needles. In fact needle phobias are not only linked to traumatic experiences amongst patients or medical providers, but also increased economic burden from missed medical procedures.

Vaccines are important for public health and safety. The World Health Organization (WHO) estimates that 2-3 million lives are saved each year due to public vaccination campaigns.

How do we as a society balance the importance of vaccines with the very real fears that many have? 

One solution is research on vaccines – and the new insights biotechnologies such as nCounter can provide. 

In this blog series, I’ll introduce how nCounter is used to make vaccines better. In this first part, I’ll discuss the development of needle-free vaccines, how researchers are working to minimize the number of pokes and improving our basic understanding of how our bodies respond to vaccines. In the second part, I’ll talk about how nCounter is leveraged to protect koalas and also to develop better vaccines for Zika and Johne’s Disease.

So, what’s nCounter? 

The nCounter system uses molecular “tags” (barcodes) and microscopic imaging to rapidly detect and count hundreds of RNA targets within a sample.

Much of the process of science relies on counting. This is an idea we’re first introduced to during school science fairs and remains critical in professional research settings.  

When researching how to make better vaccines, one thing biologists need to measure is gene expression. 

Although there is some debate over exactly what a gene is, generally genes are considered a region of DNA that codes for a protein. Proteins are a type of molecule that does a job in the cell. In the case of immunity, if you are exposed to a virus or other pathogen, certain genes “turn on” or get expressed. This leads to the production of proteins that defend the body against the invader. 

nCounter technology works by using a series of molecular probes to measure gene expression. Biologists will take a sample, such as blood cells from an animal recently given a new vaccine, and add two probes. 

The first probe is for capturing. It will bind to the target molecule which can be DNA, RNA (the intermediary between DNA and protein), or protein. The capture probe allows biologists to purify the target from the other material within the cell. 

The second probe is for detection. This reporter probe fluoresces, or gives off light when exposed to UV light. The fluorescent marker also contains a barcode for identifying which molecule is fluorescing. The light given off and accompanying barcode is then read by a computer to determine how much of a certain kind of molecule is present. 

Multiple probes can be used at the same time. A biologist could look at DNA, RNA, and protein all at once, an approach called 3D biology. This saves both precious biological material while also allowing biologists a comprehensive view of all aspects of gene expression, from the DNA to protein level. 

nCounter is a partner in needle-free and single-dose vaccines research
nCounter Technology

How is NanoString nCounter Technology Used to Make Vaccines Better? 

Needle-Free Vaccines 

The nCounter is a cost-effective technology to analyze RNA and proteins in all sample types, providing answers within 24 hours. Panels like the nCounter Host Response Panel, with its 785 targets, contain probes for human or mouse genes involved in the host response to pathogens. Ideal for vaccine research, including needle-free or single-dose research efforts.

The human immunodeficiency virus (HIV) attacks a person’s immune system. This can lead to the development of acquired immunodeficiency syndrome or AIDS. Approximately 1.2 million people in the United States have HIV. Worldwide, 37.6 million people are infected with HIV. In 2020, 690,000 people died of AIDS-related deaths. Treatment of HIV is expensive, but prevention of infection is one way to save lives and minimize economic burden.  

The development of a vaccine against HIV is one important way of preventing infection. In 2020, Bridget Fisher and colleagues published a paper on the development of a needle-free HIV vaccine

Using nCounter, Fisher and colleagues examined differences in gene expression between three different HIV vaccines. Two vaccines involved needles, one in the arm and the other in the mouth, plus a needle-free inhaled version. 

Fisher and colleagues used NanoString’s Non-human Primate Immunology Consortium Panel and Advanced Analysis Software to determine how immune system regulated genes were differentially expressed after exposure to each kind of vaccine. 

nCounter support needle-free vaccine research

Vaccines are important for public health, but the need for needles can be a turn off to many.

The authors found that either type of oral vaccination route caused a similar immune response as a standard intramuscular injection. Although the authors found that the oral injection route was slightly better than the needle-free approach, work is still progressing on optimizing the needle-less HIV vaccine. 

Single-dose Vaccines 

When SARS-CoV-2 hit the scene in late 2019, eventually leading to a pandemic in 2020, the way of life for many across the globe changed dramatically. Researchers stated that ending the pandemic would require the manufacture of many kinds of vaccines. In late 2020, both the Pfizer-BioNTech and Moderna COVID-vaccines received emergency authorization for use in the United States. Although both vaccines provided excellent protection, both versions required two doses. 

There are many reasons to seek a single-dose vaccine. Not only do people want to avoid multiple pokes, but there are also more logistical hurdles involved with ensuring people return for a second dose. Two-dose vaccines also require the manufacture of additional vaccines. This adds to an already strained system trying to manufacture the billions of doses needed to end the pandemic. 

Ruklanthi de Alwis and colleagues set out to develop an effective single-dose vaccine using self-transcribing and replicating RNA technology (STARR). The STARR technology is similar to the RNA technology in the Pfizer-BioNTech and Moderna vaccines but uses a slightly different approach to cause a more robust immune response. This may ultimately lead to achieving immunity with a single dose. 

To determine how well the vaccine worked in a mouse animal model, de Alwis and colleagues used the NanoString inflammation and immunology panels and nSolver Analysis software. Looking at blood from mice vaccinated with the new vaccine candidate, standard mRNA vaccine, and a control, the authors found that not only was the candidate vaccine successful at initiating an immune response, but that it was able to do so at a much lower dose than the standard mRNA vaccine. Although these results are still in the preclinical phase, the work by de Alwis and colleagues is an important one on the road to ending the COVID-19 pandemic. 

Basic Science Insights to Cellular Response 

Part of why researchers could develop a COVID-19 vaccine so quickly was due to decades of basic science research. Basic science research is aimed at understanding fundamental processes that will lay the groundwork for future clinical work. To improve our understanding of how a person’s immune system responds to vaccination, Catherine Collignon and colleagues studied early immune system responses to a specific vaccination platform. 

Using the nCounter NHP Immunology Panel, Collingnon and colleagues characterized changes in gene expression at one, three, and seven days post-vaccination. The authors found that there was an initial spike in key genes at days one and seven, but a dip in expression at day three. This suggests a dynamic immune response to vaccination. Using this information, researchers can create better vaccine platforms.   


In this article, I explored the science behind nCounter and how biologists are using nCounter to make vaccines better. This includes developing needle-free vaccines, reducing the necessary doses to achieve immunity, and expanding our foundational understanding of how the body responds to vaccines.

What about in specific disease contexts? In the next part of this two-part series, I’ll explore how nCounter technology is used by Australian biologists to protect koala populations from retrovirus infection. I’ll also discuss how nCounter is used to create effective vaccines against Zika and Johne’s Disease. 

For Research Use Only. Not for use in diagnostic procedures.

Post by Melanie Peffer