A team of scientists headed by researchers at the Wellcome Sanger Institute, and ETH Zürich, have created a comprehensive, first-of-its kind map detailing the network of connections that make up the human immune system. In creating what the team calls a physical wiring diagram for the immune system, the scientists show how immune cells across the body link up and communicate. The findings include the discovery of previously unknown interactions, which together shed light on the organization of the body’s immune defenses, and offer up answers to longstanding questions about current immunotherapies that are already used to treat patients. The detailed public immune system map could help lead to the development of new immunotherapies to treat cancer, infectious diseases, and other conditions where immune responses play a role.

Commenting on the resource, Jarrod Shilts, PhD, at the Wellcome Sanger Institute, said, “Meticulously isolating and analyzing every immune cell and their interactions with others has given us the first map of the conversations between all of the immune cells in the human body. This is a huge step in understanding the inner workings of the immune system and will hopefully be utilized by researchers all around the world to help develop new therapies that work with the body’s defense mechanisms.”

Shilts is first author of the researchers’ published paper in Nature, which is titled “A physical wiring diagram for the human immune system,” in which they concluded, “To our knowledge, our study is among the first to systematically map and model how the collective actions of individual receptor molecules through physical laws could explain and predict cellular connectivity on a scale as large as the circulating immune system … our work provides a systematic perspective on the intercellular wiring of the human immune system that extends from systems-level principles of immune cell connectivity down to mechanistic characterization of individual receptors, which could offer opportunities for therapeutic intervention.”

The immune system is made up of specialized cells, some of which individually travel through the body to scan for signs of injury or disease. Once these cells detect a threat, they need to communicate the message to other cells in order to mount an effective immune response. One way this cell-to-cell signaling is done is through proteins on the surfaces of cells that bind on to matching ‘receptor’ proteins on the surfaces of other cells.

“The human immune system is composed of a distributed network of cells circulating throughout the body, which must dynamically form physical associations and communicate using interactions between their cell-surface proteome,” the authors explained. “Diverse arrays of cell-surface proteins organize immune cells into interconnected cellular communities, linking cells through physical interactions that act both for signaling communication and for structural adhesion.”

Previously, scientists and clinicians only had an incomplete map of these receptor connections between all of the different types of immune cells in the body. “Despite their therapeutic potential, our map of these surface interactions remains incomplete,” the team further noted. Moreover, they pointed out, “…many immune receptors of clinical importance have been left as ‘orphans’, with their physiological ligands undiscovered despite in some cases decades of study … Without a systematic picture of the physical interactions that link immune cells, any efforts at present to generate truly systems-level views of immune function will remain patchwork at best.”

Immunotherapies have already demonstrated great potential in treating disease, most notably with certain cancers. However, these only work well in certain groups of patients and for particular conditions. An in-depth understanding of the interactions between immune cells, and how this communication fits into the human body as a whole, will be vital if researchers are to develop new effective immunotherapeutics that enhance the immune system’s ability to fight disease. A map of immune receptor connections could help explain why immunotherapies sometimes only work in a subset of patients, and offer new targets for designing future immunotherapies that may work for patients who currently do not benefit from these cutting-edge treatments.

Understanding cell-to-cell signaling in the immune system will also be necessary if we hope to prevent and treat autoimmune diseases, which are caused when the body mistakes internal signals and attacks itself.

To generate their immune cell protein interaction map the Wellcome Sanger Institute team and collaborators isolated and investigated a near-complete set of the surface proteins that physically link immune cells together. “… we first developed an optimized method for testing binary interactions of all possible pairings of recombinant surface proteins,” they wrote. “Our method, the scalable arrayed multi-valent extracellular interaction screen (SAVEXIS), simultaneously addresses several key limitations of previous methods to make it possible to screen hundreds of thousands of interactions while consuming minute amounts of protein … we systematically mapped the direct protein interactions across a recombinant library that encompasses most of the surface proteins that are detectable on human leukocytes.”

The investigators then used computational and mathematical analysis to create a map showing the cell types, messengers, and relative speed of each conversation taking place between immune cells. “By integrating our interactome with expression data, we identified trends in the dynamics of immune interactions and constructed a reductionist mathematical model that predicts cellular connectivity from basic principles.”

Creating this detailed map of the immune system required years of technological advances to tackle a problem of this scale. Each immune cell may have hundreds of distinct surface proteins and receptors on it, and the interactions involving these proteins are often so transient that specialized methods had to be invented to make assembling an accurate map possible.

The team described the development of what they term an interactive multi-tissue single-cell atlas, which “infers immune interactions throughout the body, revealing potential functional contexts for new interactions and hubs in multicellular networks.” Finally, they said “… we combined targeted protein stimulation of human leukocytes with multiplex high-content microscopy to link our receptor interactions to functional roles, in terms of both modulating immune responses and maintaining normal patterns of intercellular associations.”

With this map, it is possible to see the impact of different diseases on the immune system as a whole, and investigate new therapies that bind to different proteins on the immune cell surface. Cell surface proteins serve as the basis for new medicines more often than any other protein type, due to their accessibility to drugs and powerful influence on the signals a cell receives. And as the researchers wrote in their paper, “Because our physical wiring diagram encapsulates the diversity of surface protein architectures found across all major subsets of leukocytes, it can be integrated with publicly available expression data both qualitatively and quantitatively… More broadly, the integrated approaches that we pioneered here for disentangling the immune system provide a framework for future systematic investigations.”

Co-author professor Berend Snijder, from the Institute of Molecular Systems Biology at ETH Zürich, said, “This research has produced an incredible new tool that can be used to help highlight which proteins and pathways would be beneficial to target in drug development. It can also give insight into whether a drug will have impact on other pathways, which can cause side effects. All of this information may help in the development of new therapies and could give crucial supporting evidence to help ensure that the most effective treatments are put into clinical trials.”

Senior author professor Gavin Wright, PhD, who was previously based at the Wellcome Sanger Institute and is now at the University of York, said: “Immunotherapies work with the body’s immune system to combat diseases such as cancer and autoimmunity. They can be incredibly effective in certain groups of people, but not all, leaving some people without treatment. Our research, a culmination of over two decades of work, could hold the key to understanding why these treatments are more effective in some groups, and how they could be adapted to ensure that as many people as possible can benefit from them.”

The authors further noted, “Our analysis and the methods that we developed provide a template for future studies looking at physical cell wiring networks in detail. From these combined approaches, we may finally begin to disentangle cellular circuits in immunity and beyond, bridging from individual protein molecules to multicellular behavior.”