Scientists map networks of immune genes linked to diseases

Using new technologies to study thousands of genes simultaneously within immune cells, researchers from the Gladstone Institutes, the University of California, San Francisco (UCSF), and the 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 connect to each other are shedding light on both the fundamental drivers of immune cell function and immune diseases.

“These results help us create 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 Gladstone-UCSF Institute for Genomic Immunology and co-senior author of the new study, published in Nature Genetics.

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

Immune insights from CRISPR

Researchers know that when the immune system’s T cells—white blood cells that can fight infection and cancer—are activated, the levels of thousands of proteins in 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 affect many immune proteins at once.

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

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

Jacob Frymer, Ph.D

“We really wanted to look at what controls key immune genes,” says Jacob Frymer, Ph.D., a postdoctoral fellow in the Marson and Pritchard labs and first author of the new paper. “This kind of upstream approach has not been applied 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 painstakingly reconstructing the entire network from various satellite stations.

Frymer 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 produce a type of protein known as transcription factors. Transcription factors are the switches that turn other genes on or off and can control many genes at once. The scientists then examined the impact of disrupting these transcription factors on three immune genes known to play important roles in T cell function: IL2RA, IL-2 and CTLA4. These three genes were 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 Frymer.

An interconnected network

The researchers suspected they would find connections between the genes regulating IL2RA, IL-2, and CTLA, but were surprised by the degree of connectivity they found. 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 further fill out the immune gene map, the team followed a more traditional downstream approach, removing 24 of the well-defined regulators from the T cells to reveal the full list of genes they regulate—other than IL2RA, IL-2, and CTLA4.

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

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

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

Back to the patients

Among the full list of genes controlled by the regulators studied, the research team found a large 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 occur in different genes but – because of the regulatory connections between genes – end up having the same net effect on cells. It also pinpoints key groups 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 that network is disrupted, 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 key collections of genes that must function properly to prevent immune system disease,” Marson says.

About the research project: The article, “Systematic detection and perturbation of regulatory genes in human T cells reveals the architecture of immune networks,” was published in the journal Nature Genetics on July 11, 2022. Other authors are Cristian Garrido of Gladstone; Oren Sheik and Jessica Cortez of UCSF; and Sahin Naqvi, Nasa Sinnott-Armstrong, Arva Katiriya, 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); the Burroughs Wellcome Fund; Chan Zuckerberg’s biohub; The Innovative Genomics Institute; The American Endowment Foundation; the Institute for Cancer Research; the Jordan family; Barbara Bakar; Parker Institute for Cancer Immunotherapy; Helen Hay Whitney Scholarship; Stanford Graduate Scholarship; and the Stanford Center for Fellowship in Computational, Evolutionary, and Human Genomics.

About Gladstone Institute: To ensure our work is of greatest benefit, the Gladstone Institutes focus on conditions with profound medical, economic and social impact – unsolved diseases. Gladstone is an independent, not-for-profit life sciences research organization that uses forward-thinking science and technology to defeat disease. He is academically affiliated with the University of California, San Francisco.

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

Leave a Comment

Your email address will not be published.