New research in Nature identifies the properties of antitumor T cells, suggesting ways to boost T cell function in cancer
T cells rely on surface proteins called T cell receptors (TCRs) to bind to and destroy viruses, cancer cells, and other invaders in the body. T cells that infiltrate tumors, however, can have varied, sometimes ineffective responses. How the molecular structure and function of TCRs correlates with T cell behavior is not fully understood.
In a new study published in Nature, Giacomo Oliviera, associated researcher and institute member Catherine Wu, and colleagues at the Dana-Farber Cancer Institute and the Cancer Program at the Broad Institute of MIT and Harvard take an in-depth look at the relationship between TCRs and T cell phenotypes. Using single cell RNA (scRNAseq) sequencing and TCR sequencing (scTCRseq) of CD8+ T cells, coupled with the detection of surface proteins, the researchers set out to study the transcriptomic and molecular profiles of melanoma tumor-invading T cells and their TCRs. They found that most T cells with tumor-specific TCRs bore the molecular signs of “exhaustion,” a state of decreased function following chronic antigen exposure. Higher circulating levels of these tumor-invading, exhausted T cells in the blood correlated with persistent disease. These findings highlight the importance of restoring normal T cell function for a productive, effective immune response in cancer therapies.
In the video presentation above, Oliveira describes the research that led to the identification of the properties of antitumor T cells and highlights how such findings can pave the road to the development of novel therapeutic strategies that aim at generating T cells with potent antitumor TCRs and functional cell states.
By studying the structure of cellular receptors and of the molecules that activate them, scientists at the Universities of Geneva and Basel are deciphering the details of immune cell activation.
Chemokine receptors, located at the surface of many immune cells, play an important role in their function. Chemokines are small proteins that bind to these receptors and control the movement and behaviour of white blood cells. However, despite the importance of this family of receptors, their activation mechanism remains poorly understood. In Switzerland, a research consortium from the University of Geneva (UNIGE), the Biozentrum of the University of Basel, and the Paul Scherrer Institute (PSI) in Villigen has succeeded in decoding the activation mechanism of the CCR5 receptor, a member of this family implicated in several diseases such as HIV/AIDS, cancer, and the respiratory complications of COVID-19. This discovery represents an important step in the understanding of chemokine receptor biology, providing valuable insights for improving new drugs that this important family of receptors. This work can be found in the journal Science Advances.
The CCR5 receptor plays a major role in inflammation and immune defence, and has long been an important target for anti-HIV drugs. “Research on CCR5 began almost 25 years ago as part of the fight against AIDS”, explains Stephan Grzesiek, a professor at the Biozentrum of the University of Basel, who co-directed this work with Professor Oliver Hartley of the Department of Pathology and Immunology at UNIGE Faculty of Medicine, and colleagues from the Paul Scherrer Institute (PSI). “It is indeed fundamental to the HIV infection mechanism, but also seems to be very important in many other pathological processes, notably in cancers and inflammatory diseases. However, in order to better exploit it for therapeutic purposes, we needed to understand, at an atomic level, how activation through its binding to chemokines works.”
Chemokines are small signalling molecules that play a central role in the circulation and activation of immune cells. By binding to receptors on the membrane of white blood cells, they act as guides, ensuring that the cells reach the right place at the right time, to both maintain the immune system and respond to infection or injury. But how is the receptor able to sense the docking of a chemokine at the outside the cell? And how is this activation message transmitted to the inside of the cell so that it can respond?
Visualising atomic structures in 3D
Until now, the study of this phenomenon has been hampered by the difficulty of observing the 3D structures of the receptors when bound to the molecules that activate them. To this end, the Basel team, which specialises in structural biology, used cryo-electron microscopy tools that make it possible to preserve and observe the structure of the smallest elements of living organisms. “However, in order to understand the entire process, it is necessary to make use of engineered chemokines that bind to receptors more stably than the natural ones”, says Oliver Hartley. “For this, we were able to exploit the molecules that we had discovered in the course of our HIV drug research.” And indeed, some of these variants over-activate the receptor while others block them entirely.
The right key to fit in the lock
The receptor, which is embedded in the cell membrane, works like a “lock and key” mechanism. A specific part of the chemokine structure must fit into the CCR5 lock to activate a change in the structure of the receptor, which then lets it trigger the activation and migration of white blood cells. “The activation capacity of chemokines is determined by certain amino acids (protein building blocks) that must arrange themselves in a specific pattern. If this part of the chemokine adopts a straight shape, it succeeds in activating the receptor. But if the amino acids are changed, the molecule adopts a slightly different shape which, although it maintains a very strong bond with the receptor, prevents its activation”, explains Oliver Hartley. These small changes thus make the difference between receptor activators and inhibitors.
Better-targeted and therefore more effective drugs
Despite an almost identical architecture, minute structural differences between engineered chemokines determine their ability to activate or inhibit the receptor. A detailed understanding of this mechanism will allow for the improvement of drugs by developing new compounds capable of fine-tuning the the immune system.
It can be easy to forget that the human skin is an organ. It’s also the largest one and it’s exposed, charged with keeping our inner biology safe from the perils of the outside world.
But Michigan State University’s Sangbum Park is someone who never takes skin or its biological functions for granted. He’s studying skin at the cellular level to better understand it and help us support it when it’s fighting injury, infection or disease.
In the latest installment of that effort, Park, who works in IQ — MSU’s Institute for Quantitative Health Science & Engineering — has helped reveal how the skin’s immune cells organize themselves to ward off would-be intruders. Park and his colleagues published their work in the journal Nature Cell Biology.
“Immune cells are the soldiers of our body. In our skin, that army is maintained according to two factors: density and distribution,” said Park, an assistant professor in the College of Human Medicine’s Department of Medicine and Department of Pharmacology and Toxicology.
“We need enough immune cells to cover the whole area of our skin uniformly for proper protection. Otherwise, our skin would be vulnerable to damage and infection,” Park said. “As sensible as that might sound, it was unclear how, or even if, these immune cells were organized before this study. Many researchers thought the cells’ distribution was random.”
Skin’s immune cells have a history of being misunderstood. Many people don’t realize that our outermost layer of skin, the epidermis, is home to immune cells. And when the German scientist Paul Langerhans first discovered one type of these immune cells in the late 1800s — cells that are now called Langerhans cells — he mistook them for cells from our nervous system (to be fair, they do have a similar morphology).
To bring more clarity to how skin’s immune cells do their jobs, Park and his co-workers used state-of-the-art microscopy tools. The researchers illuminated how live immune cells arranged themselves in the skin of mice, a popular animal model with a skin biology similar to that of humans.
“IQ has so many advantages for a young investigator like me,” said Park, who joined MSU in January 2020. Just two months later, he had to start working from home due to the coronavirus pandemic. But thanks to IQ’s strong microscopy core, Park’s team was able to work almost immediately as restrictions lifted.
“I didn’t have to wait to set up microscopes in my own lab or train my students how to use them,” he said. “At IQ, we already have many different microscopes for a wide range of animal models.”
As a result, Park’s team is revealing the skin’s structure and function like never before. Having validated these new techniques and observing how immune cells are organized in the healthy skin of mice, Park’s team can start probing new questions about how skin heals.
“My lab is interested in how skin regenerates and recovers from injury,” he said. That injury could be a cut, an infection, an allergic reaction or an even more persistent disorder, such as psoriasis. “We can answer so many questions with our intravital imaging technique that you just can’t with conventional methods.”
Reference: Park, S., Matte-Martone, C., Gonzalez, D.G. et al. Skin-resident immune cells actively coordinate their distribution with epidermal cells during homeostasis. Nat Cell Biol 23, 476–484 (2021). https://doi.org/10.1038/s41556-021-00670-5
A new study that upends the idea that T cells can perfectly distinguish between healthy and infected cells may lead to improved approaches to treating cancer and autoimmune diseases.
When it comes to distinguishing a healthy cell from an infected one that needs to be destroyed, the immune system’s killer T cells sometimes make mistakes.
This discovery, described today in eLife, upends a long-held belief among scientists that T cells were nearly perfect at discriminating friend from foe. The results may point to new ways to treat autoimmune diseases that cause the immune system to attack the body, or lead to improvements in cutting-edge cancer treatments.
It is widely believed that T cells can discriminate perfectly between infected cells and healthy ones based on how tightly they are able to bind to molecules called antigens on the surface of each. They bind tightly to antigens derived from viruses or bacteria, but less tightly to our own antigens on normal cells. But recent studies by scientists looking at autoimmune diseases suggest that T cells can attack otherwise normal cells if they express unusually large numbers of our own antigens, even though these bind only weakly.
“We set out to resolve this discrepancy between the idea that T cells are near perfect at discriminating between healthy and infected cells based on the antigen binding strength, and clinical results that suggests otherwise,” says co-first author Johannes Pettmann, a D.Phil student at the Sir William Dunn School of Pathology and Radcliffe Department of Medicine, University of Oxford, UK. “We did this by very precisely measuring the binding strength of different antigens.”
The team measured exactly how tightly receptors on T cells bind to a large number of different antigens, and then measured how T cells from healthy humans responded to cells loaded with different amounts of these antigens. “Our methods, combined with computer modelling, showed that the T cell’s receptors were better at discrimination compared to other types of receptors,” says co-first author Anna Huhn, also a D.Phil student at the Sir William Dunn School of Pathology, University of Oxford. “But they weren’t perfect – their receptors compelled T cells to respond even to antigens that showed only weak binding.”
“This finding completely changes how we view T cells,” adds Enas Abu-Shah, Postdoctoral Fellow at the Kennedy Institute and the Sir William Dunn School of Pathology, University of Oxford, and also a co-first author of the study. “Instead of thinking of them as near-perfect discriminators of the antigen binding strength, we now know that they can respond to normal cells that simply have more of our own weakly binding antigens.”
The authors say that technical issues with measuring the strength of T cell receptor binding in previous studies likely led to the mistaken conclusion that T cells are perfect discriminators, highlighting the importance of using more precise measurements.
“Our work suggests that T cells might begin to attack healthy cells if those cells produce abnormally high numbers of antigens,” says senior author Omer Dushek, Associate Professor at the Sir William Dunn School of Pathology, University of Oxford, and a Senior Research Fellow in Basic Biomedical Sciences at the Wellcome Trust, UK. “This contributes to a major paradigm shift in how we think about autoimmunity, because instead of focusing on defects in how T cells discriminate between antigens, it suggests that abnormally high levels of our own antigens may be responsible for the mistaken autoimmune T-cell response. On the other hand, this ability could be helpful to kill cancer cells that mutate to express abnormally high levels of our antigens.”
Dushek adds that the work also opens up new avenues of research to improve the discrimination abilities of T cells, which could be helpful to reduce the autoimmune side-effects of many T-cell-based therapies without reducing the ability of these cells to kill cancer cells.
Reference: Johannes Pettmann et al., “The discriminatory power of the T cell receptor”, elife, 2021. DOI: 10.7554/eLife.67092
Brain tumor cells with a certain common mutation reprogram invading immune cells. This leads to the paralysis of the body’s immune defense against the tumor in the brain. Researchers from Heidelberg, Mannheim, and Freiburg discovered this mechanism and at the same time identified a way of reactivating the paralyzed immune system to fight the tumor. These results confirm that therapeutic vaccines or immunotherapies are more effective against brain tumors if active substances are simultaneously used to promote the suppressed immune system.
Diffuse gliomas are usually incurable brain tumors that spread in the brain and are difficult to completely remove by surgery. Chemotherapy and radiotherapy often only have a limited effect too. Oncologists are thus urgently trying to find innovative treatment approaches to fight the gliomas using the immune system – by means of therapeutic vaccines or immunotherapies.
Gliomas do not consist entirely of cancer cells: up to 50% of the tumor mass is made up of microglia cells – the brain’s own phagocytes – and of macrophages that enter the tumor through the blood vessels. Macrophages are also scavenger cells, but they are not effective in fighting tumor cells.
“If we are to make progress in developing immunotherapies or therapeutic vaccines, we need to understand exactly how the immune environment behaves during tumor development. Moreover, we were interested in whether special genetic features of the gliomas have a particular influence on the function of the glioma-associated immune cells,” explained Michael Platten, Director of the Department of Neurology of University Medicine Mannheim, Head of Division at the German Cancer Research Center (DKFZ), and director of the current study.
Scientists from Platten’s division have now teamed up with Marco Prinz, Medical Director of the Institute of Neuropathology in Freiburg, and his working group to publish a molecular “status analysis” of the glioma-associated immune cells. To do so, they specifically studied the RNA and protein profiles of individual microglia cells and macrophages. Using tumor models in mice, they were also able to demonstrate the development of the immune environment over the course of the disease.
Metabolic product of the glioma cells paralyzes immune cells in the brain
The researchers were particularly interested in tumors with what is known as an IDH mutation, which is found in around 70% of all low-grade gliomas. These tumor cells have an identical mutation that leads to a particular protein building block being exchanged in the IDH* enzyme.
As a result of the IDH mutation, the glioma cells release the cancer-promoting metabolic product (R)-2-HG, which, as the researchers discovered, affects the invading macrophages. These scavenger cells are reprogrammed as it were, blocking an immune response against the tumor: they release messenger substances that suppress the immune system and inhibit T cell activity – researcher refer to this as “immune paralysis”. “Ultimately, the IDH mutation enables the gliomas to protect themselves against the human immune system,” explained Mirco Friedrich, DKFZ researcher and physician at Heidelberg University Hospital, one of the lead authors of the current publication.
The researchers were subsequently able to decipher the molecular mechanism by which (R)-2-HG reprograms the macrophages: the cancer-promoting metabolic product interferes with the amino acid metabolism of the scavenger cells. This leads to activation of a central immune system regulatory molecule, aryl hydrocarbon receptor. The activated receptor causes immunosuppression of the macrophages.
Reactivating the paralyzed immune system
In view of this central role of the aryl hydrocarbon receptor, the researchers decided to specifically deactivate the function of this key molecule. To do so, they used a specific substance co-developed by DKFZ and Bayer. They combined this substance with a special immunotherapy, known as an immune checkpoint inhibitor. This immunotherapy is normally ineffective, but the combination rendered it effective in an animal model and prolonged the lives of the mice with IDH-mutant tumors.
“For the first time, we have thus demonstrated that the ‘paralyzed’ glioma-associated scavenger cells can be specifically reactivated by drugs in IDH-mutant gliomas,” Mirco Friedrich remarked. “The work is a good example of how single cell studies can lead to a treatment mechanism,” added Roman Sankowski from Freiburg University Hospital.
As Lukas Bunse, a physician at DKFZ and Mannheim University Medicine, explained, “We were recently able to prove in an early clinical study that a therapeutic vaccination** against IDH-mutant diffuse gliomas triggers the desired immune response in the study subjects. Our current studies now demonstrate how to sidestep the immunosuppressive environment in the brain and improve the effectiveness of this vaccine even further. This is an encouraging result showing that the immune system can help fight this currently almost incurable disease more effectively.” Clinical studies will now be conducted to reveal whether this treatment strategy is a promising option for glioma patients.
Mirco Friedrich, Roman Sankowski, Lukas Bunse, Michael Kilian, Edward Green, Carina Ramallo Guevara, Stefan Pusch, Gernot Poschet, Khwab Sanghvi, Markus Hahn, Theresa Bunse, Philipp Münch, Hagen M. Gegner, Jana K. Sonner, Anna von Landenberg, Frederik Cichon, Katrin Aslan, Tim Trobisch, Lucas Schirmer, Denis Abu-Sammour, Tobias Kessler, Miriam Ratliff, Daniel Schrimpf, Felix Sahm, Carsten Hopf, Dieter H. Heiland, Oliver Schnell, Jürgen Beck, Chotima Böttcher, Camila Fernandez-Zapata, Josef Priller, Sabine Heiland, Ilona Gutcher, Francisco J. Quintana, Andreas von Deimling, Wolfgang Wick, Marco Prinz and Michael Platten: Tryptophan metabolism drives dynamic immunosuppressive myeloid states in IDH-mutant gliomas. Nature Cancer 2021, DOI: https://www.nature.com/articles/s43018-021-00201-z
A particular type of dendritic cell is responsible for the tissue damage that occurs in non-alcoholic steatohepatits (NASH) in mice and humans. The dendritic cells cause aggressive, proinflammatory behavior in T cells, as now discovered by researchers from the German Cancer Research Center (DKFZ) in collaboration with colleagues from Israeli research institutes. Blocking these dendritic cells alleviates symptoms in mice. This type of approach might also prevent the development of serious liver damage in NASH patients.
Obesity is extremely widespread in the Western world, and 90 percent of those affected show signs of fatty degeneration of the liver. If they maintain an unhealthy lifestyle over a long period (high-calorie diet, sedentary lifestyle), liver cell death occurs in around a fifth of these people, resulting in inflammation of the liver, referred to as non-alcoholic steatohepatitis (NASH). NASH can lead to liver fibrosis, life-threatening liver cirrhosis and liver cancer.
In addition to its well-known role in metabolism and in filtering toxins, the liver also has a strategic function as part of the immune system, acting as the primary line of defense against all microbial toxins and food contaminants that enter the body from the intestines via the portal vein. In order to perform this task, a whole army of different immune cells patrol the liver.
“We wanted to find out which immune or inflammatory cells in the liver promote NASH and the liver damage associated with it,” explained Mathias Heikenwälder from the German Cancer Research Center (DKFZ). DKFZ researchers have now addressed the topic in collaboration with colleagues from the Weizmann Institute of Sciences and Sheba Medical Center in Israel. To do so, they analyzed the connection between the composition of the immune cell population in the liver and the degree of NASH-related liver damage. This enabled them to identify a particular type of immune cell that promotes progression of the disease – in both mice and humans.
Clue from laboratory mice on “junk food”
In order to investigate the immune system in NASH, the researchers fed laboratory mice a diet lacking essential nutrients but enriched with lipids and cholesterol – comparable to our “junk food” – and observed the development of NASH. They studied the liver immune cells using single-cell RNA sequencing and discovered an unusually high number of a particular kind of cell, known as type 1 dendritic cells (cDC1), in the liver of NASH mice.
This phenomenon was not limited to mice. In tissue samples taken from patients in liver biopsies, the researchers found a correlation between the number of cDC1 cells and the extent of liver damage typical of NASH.
Do the cDC1 cells actually have an effect on liver pathology? The researchers pursued two channels of investigation here. They studied genetically modified mice lacking cDC1. In addition, they blocked cDC1 in the liver using specific antibodies. In both approaches, lower cDC1 activity was associated with a decrease in liver damage.
Dendritic cells normally only survive for a few days and need to be continually replaced by the immune system. The researchers discovered that the NASH-related tissue damage modulates the hematopoietic system in the bone marrow, as a result of which the cDC1 precursors divide more often and replenish the supply more readily.
Dendritic cells induce aggressive behavior in T cells
In a normal immune response, dendritic cells screen the organs for conspicuous immunologic features and then continue on to the neighboring lymph nodes – the command centers of the immune response – to pass on this information to the T cells. In NASH subjects, the German-Israeli team has now discovered that the cDC1 induce inflammatory and more aggressive behavior in T cells in the lymph nodes responsible for the liver, causing liver damage and leading to progression of the disease. “It is only recently that we identified these autoaggressive T cells as being responsible for liver damage in NASH. Now we also understand what induces this harmful behavior,” Mathias Heikenwälder remarked.
Now that the cDC1 have been shown to play a key role in the progression of NASH, targeted manipulation of these cells might offer a new way of treating inflammation of the liver and its serious repercussions. “We are increasingly recognizing that certain cells of the immune system are involved in the development of different diseases, including cancer, diabetes, and Alzheimer’s disease. Medicine is thus increasingly using ways of modulating the immune system and using drugs to push it in the right direction. This kind of approach might also work to prevent serious liver damage in NASH patients,” Heikenwälder explained.
Eran Elinav, also a senior author of the study and head of research groups at DKFZ and the Weizmann Institute, believes that it is highly probable that gut bacteria affect the immune cells in this disease: “We now aim to find out how the gut and its bacteria influence activation of the immune cells in the liver. By doing so, we hope to be able to develop new treatment strategies.”
Aleksandra Deczkowska, Eyal David, Pierluigi Ramadori, Dominik Pfister, Michal Safran, Baoguo Li, Amir Giladi, Diego Adhemar Jaitin, Oren Barboy, Merav Cohen, Ido Yofe, Chamutal Gur, Shir Shlomi-Loubato, Sandrine Henri, Yousuf Suhail, Mengjie Qiu, Shing Kam, Hila Hermon, Eylon Lahat, Gil Ben-Yakov, Oranit Cohen-Ezra, Yana Davidov, Mariya Likhter, David Goitein, Susanne Roth, Achim Weber, Bernard Malissen, Assaf Weiner, Ziv Ben-Ari, Mathias Heikenwälder*, Eran Elinav*, Ido Amit*: XCR1+ type 1 conventional dendritic cells drive liver pathology in non-alcoholic steatohepatitis
Featured image: Immunofluorescence analysis of a NASH-affected human liver. DC1 cells (stained red, CD 141) patrol through the liver sinusoids (yellow, CD31). Black holes indicate lipid droplets. Source: Heikenwälder / DKFZ
Reference: Deczkowska, A., David, E., Ramadori, P. et al. XCR1+ type 1 conventional dendritic cells drive liver pathology in non-alcoholic steatohepatitis. Nat Med (2021). https://doi.org/10.1038/s41591-021-01344-3
The advance, researchers say, is like the discovery of the Rosetta stone and could eventually lead to new treatments for diseases
UCLA life scientists have identified six “words” that specific immune cells use to call up immune defense genes — an important step toward understanding the language the body uses to marshal responses to threats.
In addition, they discovered that the incorrect use of two of these words can activate the wrong genes, resulting in the autoimmune disease known as Sjögren’s syndrome. The research, conducted in mice, is published this week in the peer-reviewed journal Immunity (Cell Press).
“Cells have evolved an immune response code, or language,” said senior author Alexander Hoffmann, the Thomas M. Asher Professor of Microbiology and director of the Institute for Quantitative and Computational Biosciences at UCLA. “We have identified some words in that language, and we know these words are important because of what happens when they are misused. Now we need to understand the meaning of the words, and we are making rapid progress. It’s as exciting as when archaeologists discovered the Rosetta stone and could begin to read Egyptian hieroglyphs.”
Immune cells in the body constantly assess their environment and coordinate their defense functions by using words — or signaling codons, in scientific parlance — to tell the cell’s nucleus which genes to turn on in response to invaders like pathogenic bacteria and viruses. Each signaling codon consists of several successive actions of a DNA binding protein that, when combined, elicit the proper gene activation, in much the same way that successive electrical signals through a telephone wire combine to produce the words of a conversation.
The researchers focused on words used by macrophages, specialized immune cells that rid the body of potentially harmful particles, bacteria and dead cells. Using advanced microscopy techniques, they “listened” to macrophages in healthy mice and identified six specific codon–words that correlated to immune threats. They then did the same with macrophages from mice that contained a mutation akin to Sjögren’s syndrome in humans to determine whether this disease results from the defective use of these words.
“Indeed, we found defects in the use of two of these words,” Hoffmann said. “It’s as if instead of saying, ‘Respond to attacker down the street,’ the cells are incorrectly saying, ‘Respond to attacker in the house.’”
The findings, the researchers say, suggest that Sjögren’s doesn’t result from chronic inflammation, as long thought, but from a codon–word confusion that leads to inappropriate gene activation, causing the body to attack itself. The next step will be to find ways of correcting the confused word choices.
Many diseases are related to miscommunication in cells, but this study, the scientists say, is the first to recognize that immune cells employ a language, to identify words in that language and to demonstrate what can happen when word choice goes awry. Hoffman hopes the team’s discovery will serve as a guide to the discovery of words related to other diseases.
The immune system at war: Words and codes
How are immune cells so effective at mounting a response that is specific and appropriate to each pathogen? The answer, Hoffman says, lies in “signaling pathways,” the communication channels that link immune cells’ receptor molecules — which sense the presence of pathogens — with different kinds of defense genes. The transcription factor NFκB is one of these signaling pathways and is recognized as a central regulator of immune cell responses to pathogen threats.
“The macrophage is capable of responding to different types of pathogens and mounting different kinds of defenses. The defense units — army, navy, air force, special operations — are mediated by groups of genes,” he said. “For each immune threat, the right groups of genes must be mobilized. That requires precise and reliable communication with those units about the nature of the threat. NFκB dynamics provide the communication code. We identified the words in this code, but we don’t yet fully understand how each defense unit interprets the various combinations of the codon–words.”
And of course, calling up the wrong unit is not only ineffective, Hoffmann notes, but may do damage, as vehicles destroy roads, accidents happen and worse, as in the case of Sjogren’s and, possibly, other diseases.
Algorithms, computers and calculus: Identifying the six words
For the study, the scientists analyzed how more than 12,000 cells communicate in response to 27 immune threat conditions. Based on the possible arrangement of temporal NFκB dynamics, they generated a list of more than 900 potential “words” — analogous to all combinations of three-letter words with a vowel for the second letter.
Then, using an algorithm originally developed in the 1940s for the telecommunications industry, they monitored which of the potential words tended to show up when macrophages responded to a stimulus, such as a pathogen-derived substance. They discovered that six specific dynamical features, or “words,” were most frequently correlated with that response.
An analogy would be listening to someone in a conversation and finding that certain three-letter words tend to be used, such as “the,” “boy,” “toy,” and “get,” but not “biy” or “bey,” said lead author Adewunmi Adelaja, who earned his Ph.D. in Hoffmann’s laboratory and is now working toward his M.D. at UCLA.
The team then used a machine learning algorithm to model the immune response of macrophages. If they taught a computer the six words, they asked, would it be able to recognize the stimulus when computerized versions of cells were “talking?” They confirmed that it could. Drilling down further, they explored what would happen if the computer only had five words available. They found that the computer made more mistakes in recognizing the stimulus, leading the team to conclude that all six words are required for reliable cellular communication.
The scientists also used calculus to study the biochemical molecular interactions inside the immune cells that produce the words.
Hoffmann and his colleagues revealed in the journal Science in 2014 how and why the immune system’s B cells respond only to true threats. In a study published in Cell in 2013, his team showed for the first time that it was possible to correct a cellular miscommunication involving the connection of receptors to genes during inflammation without severe side effects.
Hoffmann’s research is supported by the National Institutes of Health.
Other co-authors of the current research are UCLA M.D.–Ph.D. student Katherine Sheu, UCLA postdoctoral researchers Yi Liu and Stefanie Luecke, and Brooks Taylor, a former UCLA doctoral student who initiated the research. All of them work or have worked in Hoffmann’s laboratory.
In the decade since the advent of CRISPR-Cas9 gene editing, researchers have used the technology to delete or change genes in a growing number of cell types. Now, researchers at Gladstone Institutes and UC San Francisco (UCSF) have added human monocytes—white blood cells that play key roles in the immune system—to that list.
The team has adapted CRISPR-Cas9 for use in monocytes and shown the potential utility of the technology for understanding how the human immune system fights viruses and microbes. Their results were published online today in the journal Cell Reports.
“This technology opens doors for identifying the human genes most important to the function of monocytes and for coming up with new therapeutic strategies against a range of pathogens,” adds co-senior author Nevan Krogan, PhD, senior investigator at Gladstone and director of the Quantitative Biosciences Institute at UCSF.
From One Immune Cell to Another
Monocytes are immune cells with a broad range of roles in defending the human body from pathogens. As part of their normal function, monocytes can give rise to two other immune cell types: macrophages, which engulf and destroy foreign material in the body, and dendritic cells, which help recognize pathogens and trigger more specific immune responses.
Marson’s team has previously studied T cells, a different class of immune cell, using CRISPR-Cas9 technology to selectively remove genes from the cells and observe the consequences. Their results have helped point toward targets for new immune therapies that make T cells more effective at fighting disease.
Monocytes, however, are notoriously hard to study in the lab. Few of the cells circulate in the blood and they behave differently in a petri dish than they would inside the body. So, applying CRISPR-Cas9 to monocytes required tweaking the standard protocols. The team had to develop an approach that would not only alter the genes inside monocytes, but ensure that those edited cells were still functional.
“Editing monocytes was challenging, but we felt it was very important to replicate the success we had obtained with T cells in other immune cells,” says Joseph Hiatt, the study’s first author and a graduate student in the Marson and Krogan labs.
A Way to Study Infections
The group showed that the monocytes edited with their CRISPR-based approach could still give rise to both macrophages and dendritic cells. To confirm whether these new edited cells behaved normally, the researchers infected cells grown in the lab with the microbe that causes tuberculosis. Macrophages originating from edited monocytes, they found, were still capable of engulfing the pathogen.
The researchers next showed that using CRISPR-Cas9 to remove the gene SAMHD1 from monocytes—and therefore the resulting macrophages—boosted more than fifty-fold the infection of cells by HIV. While SAMHD1 was already known to protect human cells from HIV, the experiment confirmed the success of their gene-editing approach in monocytes and its promise for studying diseases.
Krogan’s lab has spent recent years cataloging human proteins that viruses use to infect cells and propagate. His research has included HIV, tuberculosis,Ebola virus, and Dengue virus—viruses known to target macrophages and dendritic cells. The new ability to edit genes in these cells will help his team validate their findings and identify vulnerabilities that may help combat these diseases in the future. It could also point toward targets for drugs that help boost the ability of monocytes to fight infections, or block viruses from hijacking monocytes in the first place.
“Now that we’re confident we can edit monocytes successfully, our approach will allow us to study these cells in depth, and understand their roles in infectious diseases,” says Devin Cavero, co-first author of the study and former UCSF research associate.
Other authors are: Michael J. McGregor, Theodore L. Roth, Kelsey M. Haas, Ujjwal Rathore, Anke Meyer-Franke, Eric Shifrut, Youjin Lee, Vigneshwari Easwar Kumar, David E. Gordon, Jason A. Wojcechowskyj, Judd F. Hultquist, and Krystal A. Fontaine of Gladstone; Weihao Zheng, Jonathan M. Budzik, David Wu, Mohamed S. Bouzidi, Eric. V. Dang, Satish K. Pillai, and Joel D. Ernst of UC San Francisco; and Jeffery S. Cox of UC Berkeley.
The work was funded by the National Institutes of Health (P50 AI150476, U19 AI135990, P01 AI063302, R01 AI150449, and R01 AI124471) and the James B. Pendleton Charitable Trust.
The researchers involved are also supported in part by the National Science Foundation, a Ruth L. Kirschstein Fellowship, gifts from J. Aronov, G. Hoskin, K. Jordan, B. Bakar and the Caufield family, Gladstone, the Innovative Genomics Institute, the Parker Institute for Cancer Immunotherapy, a Career Award for Medical Scientists from the Burroughs Wellcome Fund, a Lloyd J. Old STAR award from the Cancer Research Institute, the Chan Zuckerberg Biohub, Vir Biotechnology, F. Hoffmann-LaRoche, and the BioFulcrum Viral and Infectious Disease Research Program at Gladstone.
To ensure our work does the greatest good, Gladstone Institutes focuses on conditions with profound medical, economic, and social impact—unsolved diseases. Gladstone is an independent, nonprofit life science research organization that uses visionary science and technology to overcome disease. It has an academic affiliation with UC San Francisco.
Researchers have combined genome-wide sequencing and functional profiling of immune cells to understand more about the impact of genetic variants on disease.
Certain genetic variants that cause modified protein binding in immune cells, are also seen in those at high risk of some autoimmune diseases, new research has found.
Scientists from the Wellcome Sanger Institute, Josep Carreras Leukaemia Research Institute in Spain, and the MRC London Institute of Medical Sciences (LMS) found that certain genetic variants, which alter the binding ability of a protein called PU.1 in neutrophils, are also found to be associated with auto immune disease susceptibility.
This new study, published in Nature Communications (16 April 2021), builds on previous research called BLUEPRINT. BLUEPRINT revealed how variation in blood cells’ characteristics and numbers can affect a person’s risk of developing complex diseases such as heart disease, and autoimmune diseases including rheumatoid arthritis, asthma, coeliac disease and type 1 diabetes.
This new research has provided more mechanistic detail on how PU.1 and neutrophils are impacted by genetic variation and has provided researchers a list of candidate genes that would be of interest for further research to investigate if these have a causal effect on the development of autoimmune disease.
Differences in individuals, such as risk of disease, can be influenced by a number of factors. While some of this variation is influenced by the environment and external factors such as diet, there is a substantial component driven by genetics. However, most variation is not driven through the function of a single gene but rather the sum of many subtle changes in genes or regions that control gene activity.
Previously, BLUPERINT ran large-scale genome-wide association studies (GWAS) to investigate which genetic differences are linked to changes in blood cells and if these have a link to disease. GWAS are powerful tools for identifying regions of the genome associated with human variation and diseases. However, GWAS doesn’t look at specific cell types, which makes it difficult to determine the genes that certain regions code for and the cell types they regulate.
In this new research, scientists from the Wellcome Sanger Institute, Josep Carreras Leukaemia Research Institute, Spain, and the MRC London Institute of Medical Sciences (LMS), combined previous GWAS data with in-depth functional analysis of neutrophils − a type of immune cell that make up 80 percent of the white blood cells in the body.
They found that the genetic variants that are associated with an increased risk of autoimmune disease also have an impact on binding of a certain protein in neutrophils, known as PU.1. Some genetic variants made PU.1 unable to bind to neutrophil DNA, which led to subsequent changes in gene expression and neutrophil behaviour.
While further research is needed to see if this change in the ability of PU.1 to bind directly causes certain autoimmune diseases, this research provides further understanding about the impact of these genetic variants on the cells in the body. In addition to this, the researchers suggest a list of candidate genes that could hold further information about the genetic causes of autoimmune disease.
“It is crucial to understand the mechanisms in the cell if we are to fully understand the impact of these on disease. In this case, how the genetic variants affect the ability of PU.1 binding, which goes on to modulate gene expression in neutrophils, could be vital in understanding the role that neutrophils play in certain autoimmune diseases.”
“Our work shows how mutations in the “molecular switch regions” on the DNA can lead to changes in the expression of disease-relevant genes by affecting the binding of regulatory proteins and a whole cascade of downstream events. Knowing the mechanisms by which these mutations affect cellular function brings us one step closer to being able to devise therapeutic approaches to mitigate their effects.”
“Research such as this that integrates large-scale genetic research with functional analysis gives us essential data that widen our understanding of how differences in the human genome and epigenome interact to cause devastating common diseases. Building on this understanding through further research will help inform new avenues for treating these conditions.”
— Stephen Watt,lead author and senior staff scientist at the Sanger Institute
Neutrophils play a significant role in the innate immune system, which is the body’s first line of defence against pathogens, as well as in the adaptive immune system.
Biola-Maria Javierre, Mikhail Spivakov, and Nicole Soranzo, et al. (2021) Genetic perturbation of PU.1 binding and chromatin looping at neutrophil enhancers associates with autoimmune disease. Nature Communications. DOI: 10.1038/s41467-021-22548-8.
This research was funded by Wellcome, the NIHR Cambridge Biomedical Research Centre, the UK Medical Research Council, the Spanish Ministry of Science and Innovation and by LaCaixa Banking Foundation.