Flow Cytometry in the Study of Resident T Cell Memory and Protective Immunity Against Influenza Viruses and SARS-CoV-2

This month, we are pleased to feature an interview with Dr. Carolien van de Sandt, a human virologist who works at the Sanquin Blood Bank, Amsterdam. Dr. Van de Sandt uses flow cytometry and single-cell research to study protective T cell immunity to influenza viruses and SARS-CoV-2. She and her team have recently been studying specific immunity to SARS-CoV-2, and how it develops following infection or vaccination. In this interview, Dr. Van de Sandt spoke to us about her work, her recent experience with BD’s scientific support and her vision for the future of immunology.

Tell us something about your research and your lab.

As a human viral immunologist, my research program aims to define virus-specific immunity across the human lifespan and in immunocompromised individuals. My main focus is on universal cross-strain protective T cell immunity to the seasonal, pandemics, newly emerging influenza viruses and SARS-CoV-2. I aim to understand the mechanisms that drive immunological diversity during viral infections by dissecting the molecular and functional evolution of human virus-specific immune cells, mainly CD8 (killer) T cell repertoires at high resolution. Although my research is fundamental in nature, it provides key insights into influenza virus and SARS-CoV-2 specific immunity which will helpidentify high-risk groups, predict disease outcome and ultimately improve vaccine design and pandemic preparedness. I am currently based at Sanquin in Amsterdam (The Netherlands) but also hold a position at the University of Melbourne (Australia), this allows for collaboration and sharing of knowledge and techniques. The techniques I used in Melbourne to study the SARS-CoV-2 specific immune response in COVID-19 patients are now added to the already available assays at Sanquin to study COVID-19 vaccine-induced immune responses in immunocompromised autoimmune patients in our national “Target to B” consortium, a collaboration with Prof. van Ham and Dr. ten Brinke. Needless to say, that these are incredibly large studies that can only be performed when working in a large team. We have several people in the clinic and the lab, coordinating vaccinations, sample collection, staining and freezing of immune cells, performing experiments and analysis.

What role does flow cytometry play in your work?

Flow cytometry is one of the most important tools in our work. This is how we identify virus-specific cells using tetramers and link them with other characteristics including phenotype, (poly)functionality, activation, and/or exhaustion. By studying virus-specific immune cells across different age groups, I aim to understand how these cells develop during childhood, how we maintain protective immunological memory as adults and how we lose protective immunity when we get older.

Tell us about your recent experience with BD’s scientific support for your flow cytometry panels for SARS-CoV-2 research. Why did you reach out to BD? 

We aim to get an in-depth understanding of how protective immunity against SARS-CoV-2 infection and vaccination develops and how long protective immunity is maintained. In other words, how long after infection or vaccination are you still protected from a new infection. We study different arms of the immune system including innate, humoral and cellular immunity. These kinds of studies require a lot of fluorescent markers, of which BD is one of the leading developers.

Was this the first time you reached out to BD’s scientific support?

Yes, recent developments (BD FACSymphony™) allow us to analyse bigger fluorescent panels which include up to 24 markers. These panels take a lot of time to design and optimise. As this is a COVID-19 related study we wanted to set up the panels as quickly and efficiently as possible, which was made possible with the help of the BD scientific support team.

How did the panels perform? 

We were aware that by including 24 markers- we would be pushing the limits of the number of markers we could detect, but with the advice of the BD support team and with some minor tweaks while titrating and testing the panels, we were able to set up and validate those panels in a short timeframe and we were very happy with the results. The panels worked well.

What was the biggest added value for you? 

Friendly service that allowed us to set up very extensive and complicated panels in a short timeframe, which is essential for our COVID-19 study. 

What role do you think technologies like Multi-omics can play in immunology research? Do you think such technologies can complement flow cytometry?

From personal experience, I know that a multidisciplinary approach can be very valuable. I use the state-of-the-art multidisciplinary genotype-to-phenotype platform (developed in the Kedzierska lab at the University of Melbourne) to decipher the molecular and functional evolution of human CD8 T cell repertoires. This genotype-to-phenotype platform integrates high-dimensional analysis of antigen-specific T cells using tetramers in combination with phenotypic flow cytometry, single-cell index sorting, followed by single-cell T cell receptor (TCR) multiplex and/or single-cell transcriptomics. This allows us to link phenotypic characteristics with their respective TCRs and gene expression profiles, as index-sorting “remembers” the exact phenotype of individual cells. This in turn allows us to understand which cells expand and/or exert the largest immune function or get exhausted. Combining these different technologies allows us to perform an in-depth analysis of relatively small human samples.

What is your view on SARS-CoV-2 and the current state of research in the area? What do you think about the vaccines available and their efficacies?

Many virologists, including myself, had predicted that there would be a major pandemic within the coming years and that the prime suspects for causing such a pandemic would be either an influenza virus or a coronavirus. Hence, many years of pre-pandemic influenza and/or coronavirus research made rapid development of the current COVID-19 vaccines possible. However, there is still a lot unknown. One of the most important questions is how long the COVID-19 vaccines will provide protection and whether they protect against variants of the virus. It is in the line of expectations that like with the influenza virus, SARS-CoV-2 gradually changes over the years and at some point, the virus will be so different from the variant used for the vaccine development that the vaccine will need to be updated. In my opinion, the Holy Grail is to develop a universal COVID-19 or influenza vaccine which will protect againstthe currently circulating virus, to future variants of the virus as well as to new, related viruses introduced in the human population and which, thus, will provide protection during the next pandemic outbreak.

What’s your vision for the future of immunology?

The current developments in immunological techniques, including large panel flow cytometry especially when combined with other multidisciplinary platforms like single-cell sequencing, will form the basis for fundamental research which will provide new insights into protective and detrimental immunity in both healthy individuals and high-risk groups including the elderly and immunocompromised individuals. This knowledge will be leveraged to allow for a better prediction of disease outcome, treatment and vaccination strategies for viral infections (e.g. influenza virus and SARS-CoV-2 allowing us to be better prepared for the next pandemic), autoimmune diseases, transplantations and cancers. 

Any recommendations for BD or BD’s scientific support?

Providing the opportunity to combine fluorescence and barcoding techniques for a more in-depth analysis of phenotypic markers.

The scientific support was excellent, friendly, fast and accurate.

^{The views expressed by the interviewee are her personal opinions.}