Scientists map disease-related immune gene networks

Using new technologies to study thousands of genes simultaneously within immune cells, researchers at the Gladstone Institute, UC San Francisco (UCSF) and Stanford School of Medicine have created the most detailed map yet of how complex networks of genes work together. New insights into how these genes relate to each other shed light on both the basic drivers of immune cell function and immune diseases.

“These results help us draw a systematic network map that can serve as an instruction manual for how human immune cells work and how we can engineer them to our advantage,” says Alex Marson, MD, PhD, director of the Gladstone Institute-UCSF. of Genomic Immunology and co-author of the new study, published in Nature Genetics.

The study, conducted in collaboration with Jonathan Pritchard, PhD, professor of genetics and biology at Stanford School of Medicine, is also critical to better understanding how variations in a person’s genes relate to autoimmune disease risk.

Immune insights from CRISPR

Researchers know that when the immune system’s T cells – white blood cells that can fight infections and cancer – are activated, the levels of thousands of proteins inside the cells change. They also know that many of the proteins are interconnected so that changes in the level of one protein can cause changes in the level of another.

Scientists represent these connections between proteins and genes as networks that look somewhat like a subway map. Mapping these networks is important because they can help explain why mutations in two different immune genes can lead to the same disease, or how a drug can have an impact on many immune proteins at the same time.

In the past, scientists have mapped parts of these networks by removing the gene for each protein, one at a time, and studying the effect on other genes and proteins, as well as on overall immune cell function. But this kind of “downstream” approach reveals only half the picture.

We really wanted to look at what controls key immune genes.

Jacob Freimer, PhD

“We really wanted to look at what controls key immune genes,” says Jacob Freimer, PhD, a postdoctoral fellow in the Marson and Pritchard labs, and first author of the new paper. “This kind of upstream approach had not been done before in primary human cells.”

This upstream approach would be like mapping subway routes by first identifying major hubs and then determining routes to those key stations, rather than carefully reconstructing the entire network from various satellite stations.

Freimer and his collaborators turned to the CRISPR-Cas9 gene-editing system, which allowed them to disrupt thousands of genes at once. They focused on genes that make a type of protein known as transcription factors. Transcription factors are switches that turn other genes on or off and can control many genes at the same time. The scientists then studied the impact of disrupting these transcription factors on three immune genes known to play an important role in T-cell function: IL2RA, IL-2 and CTLA4. These three genes were the hubs that anchored upstream mapping efforts.

“This allows us to go through over a thousand transcription factors and see which ones have an impact on these immune genes,” says Freimer.

An interconnected network

The researchers suspected they would find links between the genes that regulate IL2RA, IL-2 and CTLA, but they were surprised by the extent of the connection they discovered. Among the 117 regulators found to control the levels of at least one of the three genes, 39 controlled two of the three, and 10 regulators simultaneously changed the levels of all three genes.

To help complete the immune gene map even more, the team then took a more traditional downstream approach, removing 24 of the pinpointed regulators from T cells to show the full list of genes they regulate—except IL2RA, IL-2 and CTLA4. .

The researchers showed that many of the regulators checked each other. The transcription factor IRF4, for example, altered the activity of 9 other regulators and was itself regulated by 15 other regulators; all 24 controlled IL2RA levels. In other cases, the regulators were themselves regulated by IL2RA, in so-called “feedback loops”.

As in a dense subway network, each center connected to many others, and connections ran in both directions.

“There were cases where a transcription factor regulated IL2RA, but then IIL2RA itself also controlled the same transcription factor,” says Freimer. “It appears that these types of feedback loops and regulatory networks are much more interconnected than we previously realized.”

Return to Patients

Among the full list of genes controlled by the regulators studied, the research team found a high number of genes already associated with immune diseases, including multiple sclerosis, lupus and rheumatoid arthritis.

The new map helped reveal how the genetic changes associated with these diseases can appear in different genes, but — because of regulatory connections between genes — end up having the same net effect on cells. It also points to key sets of genes that can be targeted by drugs to treat immune diseases. The study suggests that there is a central network of important genes, and when this network is disturbed, it can increase a person’s risk of disease.

“When we understand the ways in which these networks and pathways are connected, it begins to help us understand the key collections of genes that must function properly to prevent immune system disease,” says Marson.

About the Research Project: The paper “Systematic detection and perturbation of regulatory genes in human T cells reveals architecture of immune networks” was published in the journal Nature Genetics on July 11, 2022. Other authors are Christian Garrido of Gladstone; Oren Shaked and Jessica Cortez of UCSF; and Sahin Naqvi, Nasa Sinnott-Armstrong, Arwa Kathiria, Amy Chen and William Greenleaf of the Stanford School of Medicine. The work and authors were supported by the National Institutes of Health (R01HG008140, RM1-HG007735, T32AI125222 and 5F32GM135996-500 02); Burroughs Wellcome Fund; Chan Zuckerberg Biohub; Institute of Innovative Genomics; American Endowment Foundation; Cancer Research Institute; the Jordan family; Barbara Bakar; Parker Institute for Cancer Immunotherapy; a Helen Hay Whitney Fellowship; a Stanford Graduate Scholarship; and a Stanford Center for Computational, Evolutionary, and Human Genomics Fellowship.

About the Gladstone Institute: To ensure our work does the greatest good, the Gladstone Institute focuses on conditions with profound medical, economic and social impact—unsolved diseases. Gladstone is an independent, not-for-profit life science research organization that uses visionary science and technology to overcome disease. She has an academic affiliation with the University of California, San Francisco.

About UCSF: The University of California, San Francisco (UCSF) is exclusively focused on the health sciences and is dedicated to promoting health worldwide through advanced biomedical research, graduate-level education in the life sciences and health professions, and excellence in care. to patients. UCSF Health, which serves as UCSF’s primary academic medical center, includes top-ranked specialty hospitals and other clinical programs, and has connections throughout the Bay Area.

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