Danish researchers have developed a molecular biology tool to illuminate the immune cells when the immune system is active. The tool may provide completely new insight into the immune response to harmful pathogens such as SARS-CoV-2, the new coronavirus.
The immune system mobilizes thousands of cells when it actively combats viral infections.
If researchers want to understand the processes involved so they can optimize the development of medicine and vaccines, they need tools to examine the immune system in detail while it is active.
In a new study, Danish researchers showed that they can use these tools to illuminate the immune cells. Researchers can then use a laser to count which cells proliferate when the immune system actively counteracts external threats.
“You could say that we have inserted a biomarker in the genome to investigate how the immune system works. With our new method, we can study how the immune system functions much more easily than by using a microscope, for example,” explains Søren Egedal Degn, Assistant Professor, Department of Biomedicine, Aarhus University.
The research has been published in Cytometry Part A.
The immune system in an eternal arms race
Understanding the research results requires understanding how the immune system works.
When the immune system encounters a foreign body, it must mount a defence based on immune cells that can recognize the threat that is invading the body.
The immune system has thousands of different immune response cells that can recognize antigens on viruses, bacteria or other pathogens, but only a few can respond to any individual pathogen, such as the SARS-CoV-2 virus.
When these few immune cells recognize SARS-CoV-2 as an external threat, they begin to proliferate furiously to boost the counterattack; this is called clonal expansion.
“Clonal expansion results from viruses and bacteria developing much more rapidly than we do. That is why we have developed this immune response in which we do not need to have all the immune cells operating at full speed all the time. Instead, we can rely on the required cells to start proliferating to respond to a threat. This is like Agent Smith from The Matrix. He begins to clone himself when the protagonist Nemo shows his superiority in one-to-one combat,” says Søren Egedal Degn.
Lacking tools to understand clonal expansion
Part of the clonal expansion process involves the immune cells being able to recognize the body’s own cells and thereby create an autoimmune response, such as in several autoimmune diseases, including type 1 diabetes, multiple sclerosis, rheumatoid arthritis and systemic lupus erythematosus.
In the arms race between our immune system and the pathogens, we produce immune cells in countless variants, and then the immune system screens the cells to eliminate those that can attack the body.
The only ones remaining are those that can potentially counteract external threats.
“This has been the fundamental understanding of the immune system for the past 70 years, but we lack tools to study clonal expansion to better understand how the immune system functions,” says Søren Egedal Degn.
Illuminating the immune response
Søren Egedal Degn is striving to develop tools to study clonal expansion.
In the new research, the researchers from Aarhus University inserted fluorescent genetic markers into the genome of mice, thereby tagging the mice’s immune cells with dye.
This means that if the immune system is activated to counteract viruses or bacteria, more and more immune cells with a specific colour or colour combination will be formed.
Visually, this means that more of the types of cells that have been activated in the counterattack will be represented in the colour distribution of a blood sample or of a cell sample from a mouse, and the researchers can see this.
“This enables us to monitor the timing and location of clonal expansion. We can determine how the distribution of immune cells develops over time and where in the body the immune response is strongest. Of course, some colours will be more frequent in the lymph nodes, which play a key role in activating the immune system,” says Søren Egedal Degn.
Firing a laser at living tissue
However, examining these phenomena with a microscope and in tissue from live mice can be cumbersome.
Søren Egedal Degn’s research team, led by postdoctoral fellow Cecilia Fahlquist-Hagert, has therefore developed a method to quickly count how many coloured cells of a specific type are in a sample.
The researchers use flow cytometry and imaging flow cytometry, which fire lasers at the biological samples and simultaneously produce fluorescent images of the samples, which are then analysed for the number of coloured dots.
Combining this with advanced computer algorithms to analyse the images enables the researchers to identify populations of specific immune cells and monitor the timing and location of their activity.
“Relating to all the data that can be extracted from the samples can be difficult, but we can use smart algorithms to visualize this in 2D and preserve the complexity of the data set,” says Cecilia Fahlquist-Hagert.
Søren Egedal Degn expects that this new way of studying clonal expansion will enable researchers to advance their knowledge about the immune system, which will enhance the potential for developing medicine and vaccines.
Explaining the transmission of autoimmune diseases
The researchers already used this technique to distinguish between two types of immune response: one targeting a pathogen and one targeting the body itself.
The aim was to see whether the response time of the immune system differed.
The results showed that the immune system reacted equally quickly in both cases. According to Søren Egedal Degn, this suggests that, once the immune system has crossed the barrier for tolerance of the body’s own cells, it proceeds to avidly destroy all cells it encounters – foreign and domestic.
According to Søren Egedal Degn, this may explain why some autoimmune diseases such as rheumatoid arthritis and systemic lupus erythematosus develop and spread from one tissue to another.
“We think the reason is that, once the brake has been released and the process initiated, new immune cells are constantly being created that react with one antigen after another, and these antigens can be in the body’s own tissue,” explains Søren Egedal Degn.
“Seeing the confetti colors in a new light utilizing flow cytometry and imaging flow cytometry” has been published in Cytometry Part A. In 2019, the Novo Nordisk Foundation awarded a grant to Søren Egedal Degn for the project Mechanisms Governing Breakdown of Tolerance at the Germinal Centre Checkpoint.