Scientists Map Network of Disease-Related Immune Genes

“These results help us refine a systematic network map that can serve as an instruction manual on how human immune cells function and how we can engineer them to our advantage,” said Alex MarsonMD, PhD, director of the Gladstone-UCSF Institute of Genomic Immunology and senior author of the new study, published in Natural Genetics.

The study, which was carried out in collaboration with Jonathan PritchardPhD, professor of genetics and biology at Stanford School of Medicine, is also important for better understanding how variations in a person’s genes are related to the risk of autoimmune diseases.

Immunity Insights from CRISPR
Researchers know that when the immune system’s T cells—white blood cells that can fight infection and cancer—become active, the levels of thousands of proteins in the cells change. They also know that many proteins are interconnected so that a change in the level of one protein can cause a change in the level of another.

Scientists represent the relationship between these proteins and genes as a network that looks like a subway map. This tissue mapping is important because it can help explain why mutations in two different immune genes can cause the same disease, or how a drug can impact many immune proteins at once.

In the past, scientists have mapped parts of this network by deleting the genes for each protein, one at a time, and studying their impact on other genes and proteins, as well as the overall function of immune cells. But this kind of “downstream” approach reveals only half of the picture.

“We really wanted to see what controls key immune genes,” said Jacob Freimer, PhD, a postdoctoral fellow in Marson and Pritchard’s laboratory, and first author of the new paper. “This kind of upstream approach has never been done before in primary human cells.”

This upstream approach would be like mapping subway routes by first identifying major hubs and then figuring out routes to those major stations, rather than painstakingly reconstructing the entire network from different satellite stations.

Freimer and his collaborators turned to the CRISPR-Cas9 gene-editing system, which allows them to disrupt thousands of genes at once. They concentrated on the genes that make a type of protein known as a transcription factor. Transcription factors are switches that activate or deactivate other genes and can control many genes at once. The scientists then studied the impact of this disruption of transcription factors on three immune genes known to play important roles in T cell function: IL2RA, IL-2, and CTLA4. These three genes are the hubs that anchor upstream mapping efforts.

“This allows us to trace over a thousand transcription factors and see which ones impact these immune genes,” Freimer said.

Connected Network
The researchers expected that they would find an association between the genes that regulate IL2RA, IL-2, and CTLA, but they were surprised by the level of connectivity they found. Among the 117 regulators found to control the level of at least one of the three genes, 39 controlled two of the three, and 10 regulators simultaneously altered the level of all three genes.

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

The researchers point out that multiple 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 levels controlled IL2RA. In other cases, the regulator itself is regulated by IL2RA, in what is called a “feedback loop.”

As in a congested subway network, each hub is connected to many other hubs, and the connection goes both ways.

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

Back to Patient
Among the comprehensive list of genes controlled by the regulator studied, the research team found a large number of genes already linked to immune diseases, including multiple sclerosis, lupus, and rheumatoid arthritis.

The new map helps reveal how the genetic changes associated with the disease may appear in different genes but—because of regulatory connections between genes—end up having the same net effect on cells. It also points to a key group of genes that drugs might target to treat immune diseases. This study shows there is a central network of important genes, and when this 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 the key gene pools that need to function properly to prevent disease in the immune system,” Marson said.

About the Research Project
The paper “Systematic discovery and disruption of regulatory genes in human T cells reveals immune network architecture” published in the journal Natural Genetics on 11 July 2022.

Another author is Christian Garrido from Gladstone; Orange Shaken and Jessica Cortez from UCSF; and Sahin NaqviNasa Sinnott-Armstrong, Spirit of Katharia, Amy Chenand William Greenleaf from the Stanford School of Medicine.

Work and authors supported by the National Institutes of Health (R01HG008140, RM1-HG007735, T32AI125222, and 5F32GM135996-500 02); Burroughs Wellcome Fund; Chan Zuckerberg’s biohub; Institute of Innovative Genomics; American Endowment Foundation; Cancer Research Institute; Jordanian family; Barbara Bakar; Parker Institute for Cancer Immunotherapy; Helen Hay Whitney Scholarship; Stanford Graduate Scholarships; and the Stanford Center for Computational, Evolutionary, and Human Genomics Fellowship.

About Gladstone Institutes
To ensure our work produces the greatest good, Gladstone Institutes focuses on conditions with profound medical, economic, and social impacts—unsolved diseases. Gladstone is an independent, non-profit life science research organization that uses visionary science and technology to tackle disease. It has academic affiliation with University of California, San Francisco.

About UCSF
It 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 patient care. UCSF Health, which serves as UCSF’s premier academic medical center, includes top-ranking specialty hospitals and other clinical programs, and has affiliates throughout the Bay Area. Learn more at ucsf.edu, or check out our Fact Sheet.

Source
Gladstone Institute: Julie Langelier | [email protected] | 415,734.2019

UCSF: Robin Marks | [email protected] | 628.399.0370

SOURCE University of California, San Francisco; Gladstone Institute

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