High-dimensional flow cytometry and Multi-Omics at the frontiers of immunology – Interview with Prof. Ido Amit, Immunology Department, Weizmann Institute of Science, Israel

In our continuing coverage of expert opinions about the frontiers of immunology, we are pleased to present an interview with Prof. Ido Amit of the Weizmann Institute of Science, Israel. Prof. Amit’s lab uses cutting-edge flow cytometry and novel single-cell genomic technologies to investigate a variety of questions about cancer immunotherapy, development, the brain, metabolism and autoimmunity. In this interview, Prof. Amit talked to us about his lab, his recent work on the TREM2 pathway and its implications in Alzheimer’s disease, his views on high-dimensional flow cytometry and its role in Multi-Omics, and his vision for the future of immunology.

  1. Tell us something about your research and your lab.

My lab in the Immunology Department of Weizmann Institute focuses on developing the next frontier in single-cell genomic approaches, to define the role of immune cells and their function in diverse pathologies and tissues. The field of single-cell genomics and its application for immunology was initiated about 10 years ago. We are very happy to see how single-cell genomics has developed hand-in-hand with advances in flow cytometry approaches. These are pushing the boundaries of understanding of the immune cells and the different markers and pathways of immune cell subsets.

  1. You recently published some interesting work on the TREM2 signalling pathway, and its potential therapeutic applications. Tell us more about this work.

One of the challenges of understanding and defining the role of the different immune cell subsets and pathways in pathologies is going back to the fundamental challenge of defining an immune cell. Why do we call a certain cell a dendritic cell or a T cell? If we go back in time, some 150 years ago, a Russian scientist named Elie Metchnikoff observed that there were specific cells that performed immune functions like engulfing pathogens and dead cells.  He later called these cells macrophages. In these early days, the cell types were defined by their function. In recent years, we have moved forward by using flow cytometry and monoclonal antibodies to define immune subsets based on markers. If you look in hindsight, there is no single attribute to define a cell type. It is based on their morphology, structure, function, a few cellular markers and tissue location. It is challenging to use these parameters if we consider immune cells that are constantly changing due to their environment, if they move to a new tissue or if they see a pathological site that is activated by cell death, cytokines or other factors. The use of single cell genomics is game-changing as it enables us to have a uniform platform on which we can overlay all the cells and differentiate between them based on their differential transcription activity. This capability has allowed us to look into different pathological sites, whether it is an Alzheimer’s model or cancer one. Using this technology, we started seeing that the markers that we were using to differentiate between different cell sub-populations were not accurate. We were not capturing homogeneous groups of cells. In the initial discovery of the role of TREM2-specific microglia in Alzheimer’s disease, we found a TREM2 signature that included many other receptors and checkpoints. We found that this population of microglia represented the essential differentiator between the neurodegenerative and non-neurodegenerative (wild type) mouse model. The resident immune cells (microglia) in the brain were responding to the pathological insult and upregulating the TREM2 pathway. This finding of a new innate immune signaling hub, involved in sensing neurodegeneration opened a new area in the immunology field. What was intriguing is that many of the genes associated with these microglia (which we named DAM or Disease-Associated Microglia) were correlated in human cohorts that suffered from Alzheimer-like symptoms. The same genes were extremely enriched in the human cell population, tying up the human pathology with this specific immune subset and pathway.

At that point, it was not fully clear whether these cells were good or bad. When you have a pathology, the enriched subset could either be counteracting the damage or pathology, or contributing to it. To make a long story short, based on the genetic studies we did, we could tell that this was a protective mechanism. We found that this was the mechanism the body uses to fight the damage to the brain. This correlated well with the human data which showed that inactivation of TREM2 and the other genes in the TREM2 pathway contributed to the increase of the disease while their activation did the exact opposite. This is how the combination of single-cell genomics and FACS/cell sorting approaches allowed us to define a new subset of immune cells and their markers that were protecting the brain from Alzheimer’s disease. This also suggested to us that the activation of TREM2 could be potentially used in therapeutics. 1,2

Later on, we found that TREM2 is important for more than just Alzheimer’s. Our subsequent research on obesity and cancer revealed that TREM2 is a major signaling hub responding to pathological cues in the body. As in the brain scenario, we noticed that TREM2 was also playing this protective role in atherosclerosis and obesity. It detects different types of ligands that are associated with cell death and once this happens, it brings about several tissue protection functions like lipid metabolism and phagocytosis to repair the damage. It also has a very strong immunosuppressor function. You would not want these pathologies or damages to increase the activity of the immune system as that would lead to a vicious cycle and increased damage to the brain.  We hypothesized that the combination of damage detection and immune suppression would be a bad scenario in the case of tumors where you want an active and aggressive immune response. We also saw that many of these markers that define tumor-suppression were intracellular, so we developed a new single-cell technology called INs-seq. Using this new technology, we labelled the intracellular proteins, and then using FACS, we sorted the cells and isolated those with high activity. Sequencing these cells allowed us to align the activities to the specific transcriptome and cell subset. We used this technology to study TREM2 in tumors to see if we could do the opposite of what we would want it to do in the brain, which is to activate cytotoxic T cells to reactivate an effective anti-tumor immune response. Thus, we showed the huge potential to use TREM2 based therapeutics to reactivate the immune system towards currently unresponsive tumours.1,2

  1. What are your views about multi-omics and scRNA sequencing? Do you think the data generated from this technique can complement flow cytometry?

‘Complementary’ is exactly what we should be thinking about. It’s not like the microfluidic ‘omics’ approaches are replacing FACS. On the contrary, these are other toolsets to characterise immune cells. I think the more we start combining them, the more we are going to enhance our understanding of the pathology, biology and the application of these technologies for human health. There are very large advantages of sorting technologies, concerning the speed, depth (identifying even extremely rare cells) and accuracy to which one can use it to characterise the immune system. There is no replacement for that. The breadth of the genes that can be characterised using the single-cell approaches is not possible with FACS, even with the new advanced multi-parameter sorters – hence we must innovate to combine and merge the two technologies. The future will be to combine large gene atlases across large patient cohorts and overlay them with more and more layers of information from chromatin signaling, temporal, spatial gene expression and so on.  As for the choice between using sort-based or sequencing-based technologies, the lines are going to become a lot less clear and we will be merging them in many ways. It will become such that you will have a complete set of markers defining each region of the atlas. You would want to focus on streamlining the atlas by using FACS to characterise specific markers, combine them, sequence the cells, and go on to understand their chromatin or their specific signalling so you can develop drugs for them. I think we are going to see more and more merging of these approaches and improved algorithms for integrating these increasingly larger databases on a single grid. I think it is going to be a very bright future for science, immunology and the technology communities working with these approaches. This kind of research will allow us to understand the immune system and how it works in individual patients. You can see that the COVID situation is really pushing us towards this kind of research. We need to work forcefully to merge the single cells genomics and FACS based technology, and the new tools emerging (like the BD FACSymphony™ S6) make me very optimistic that this is where we are heading. While the immune system knows its situation, we still cannot distinguish between patients who may get devastating COVID and those who will get a mild one or, patients that will respond to immunotherapy and those that will not. The information is all there and it’s all in the activity of the immune cells. We still have a long way to go but I am very optimistic we will see large leaps in this kind of research in the coming few years. This new era of single-cell technologies combined with FACS will give us answers.

  1. You recently purchased a BD FACSymphony™ S6. Which features of the system help you most with your research and do you have any ideas in which direction flow cytometry should develop?

I think the S6 is a very important upgrade to our toolset going in this direction, which is to combine sorting, specifically multiparameter index sorting and single-cell genomics. There are many unique new features in the BD FACSymphony™ S6 that make it a huge upgrade from the BD FACSAria™ for the single-cell genomics community. These include, first and foremost, the ability to sort much faster. We see an order of magnitude increase in sorting speed between the BD FACSymphony™ S6 and the previous generation. That’s very important. One can think of it as ten for the price of one. The ability to index sort intuitively was not so much built into the previous version of the BD FACSDiva™ software and that made it quite challenging to use a real-time gating to select the population and also to do index sorting without hampering the ability to collect the cells. Activating the index sorting mode would slow down the instrument considerably. With the BD FACSymphony™ S6, index sort is intuitively integrated into the software and so the data can be collected without slowing down the instrument. Last but not the least, there is the ability to focus or zoom in on a specific sub-population using a wide number of molecular characteristics, scaling to 30-40 markers. In this era, we have gone into dissecting the immune system much more finely into different myeloid subpopulations with specific activities and that’s really a game-changer. I believe the BD FACSymphony™ S6 is the first instrument for this multi-omics era which will hugely drive this community further. So, the next time there is a COVID-like situation, we will be armed with all the basic research results obtained through such instrumentation, that could play a role in helping detect at the molecular level which patients are going to do well and which aren’t. Generally, we need a rapid buildup of basic knowledge that we can use in the clinic for personalised immune monitoring and treatment at a later stage. This is the first instrument that lets us carry out the basic research that will allow us to think about such clinical research capabilities.

  1. What are your views on the immunology of the SARS-CoV-2 virus and the current state of research in the area? What do you think about the vaccine candidates that are nearing approval?

I think vaccines are very important and highlight the achievements of immunology and science in general. These vaccines are giving everyone hope for a normal life and I don’t know where we would be without them. This is one solution but not the complete solution. What we see now is the result of 30 years of investment in understanding the immune system and how to generate effective vaccines and RNA vehicles. The explosion of new research driven by the single-cell genomics tools will eventually enable us to pinpoint the new mechanism that leads to the pathology and it will enable a surge of new and more potent drugs to target it. The BD FACSymphony™ S6 instrument can be a new and very important driving force to lead this research.

  1. What do you see as the most important developments in immunology at the moment and in the future. What is the direction?

It’s a good question. I think everyone has their own opinion about this. I can say that in general, in this era of immunology, Multi-Omics is a very strong driver of understanding how the immune system functions, and more so, how it dysfunctions in pathology. The developments that provide a deep molecular handle on the different immune subsets, and their interactions and signaling across a large number of patients and how they impact the disease are going to be critical. Currently, we know how to block certain pathogenic cytokines like TNF (e.g. in autoimmunity), but what if we knew how the immune system repairs the scarred areas? Not just the cytokines but also the immune cells and signaling involved in fixing the tissue and bringing it back to its healthy homeostatic state, so that the disease does not come back. We are going to probably know much more about how to control the immune system for beneficial purposes; reactivate the immune system in cancer, not only in melanoma but also in others like lung and breast cancers.

1 Katzenelenbogen Y, Sheban F, Yalin A, Yofe I, Svetlichnyy D, Jaitin DA, Bornstein C, Moshe A, Keren-Shaul H, Cohen M, Wang SY, Li B, David E, Salame TM, Weiner A, Amit I. Coupled scRNA-Seq and Intracellular Protein Activity Reveal an Immunosuppressive Role of TREM2 in Cancer. Cell. 2020 Aug 20;182(4):872-885.e19. doi: 10.1016/j.cell.2020.06.032.
2 Deczkowska A, Weiner A, Amit I. The Physiology, Pathology, and Potential Therapeutic Applications of the TREM2 Signaling Pathway. Cell. 2020 Jun 11;181(6):1207-1217. doi: 10.1016/j.cell.2020.05.003.
Disclaimer: The views presented by the interviewees are their personal opinions.
BD, the BD Logo, FACSDiva and FACSymphony are trademarks of Becton, Dickinson and Company. © 2021 BD and its subsidiaries. All rights reserved.
BD FACSymphony S6 and BD FACSAria™ III are Class 1 Laser products.
BD FACSAria™ II is discontinued.
Products are for Research Use Only. Not use in diagnostic or therapeutic procedures.


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