Immune system memory discovery suggests new approaches to control inflammation

Sometimes you can learn a lot by coming at things from a fresh angle. Research associate Tianhao Duan, PhD, and his colleagues present a perfect example of how it happens. And what they found out not only helps revise scientific understanding of how the body’s natural defenses work, but also may influence treatment for the many illnesses caused when those defenses kick into dangerous overdrive.

“A lot of diseases are associated with inflammation, such as rheumatoid arthritis, type 2 diabetes and even certain cancers,” said Duan, a member of the lab led by Rongfu Wang, PhD, a professor of pediatrics and medicine at the Keck School of Medicine of USC. “Even with COVID-19 patients, virus-triggered hyperinflammation is the primary and direct cause of severe disease and fatalities, rather than the coronavirus itself. Therefore, understanding how the regulatory mechanisms governing inflammation processes within our body is critically important.”

The immune system has two complementary branches: There’s the adaptive, which “learns” to recognize threats based on past illness and vaccination. But before the adaptive immune system works, there’s the innate immune system, the first line of barriers and responses each person is born with, long thought to lack that learning ability.

But in recent years, science has upended that assumption, with new research showing the innate immune system does indeed have its own type of memory, and it plays two roles — it can aid in responding to reinfection or it can help suppress an immune response, known as innate immune tolerance.

The discovery of this memory and its dual features inspired Duan and his colleagues to explore innate immune memory further for new insights and to inform medical practice.

Most research on innate immune memory has focused on genes and the set of epigenetic changes that modify how they’re expressed, but Duan and his team chose a seldom-traveled route. They are exploring posttranslational modifications — changes that happen further down the line, after DNA blueprints have been translated into proteins — on the chance that answers lie where few others are asking questions.

This is the approach behind a recent study in the journal EMBO Reports led by first author Duan and corresponding author Wang, who is also the Endowed Chair in Cell Immunotherapy Research and director of the Cell Immunotherapy Program at Children’s Hospital Los Angeles and co-director of the Tumor Microenvironment Program at USC Norris Comprehensive Cancer Center.

They found that one enzyme in particular, USP3, plays a role in teaching the innate immune system to mute its response to some threats — a discovery with implications for treating sepsis, a potentially fatal result of infection.

One tale of how the innate immune system learns

The study, funded in part by the National Institutes of Health, tells a story of an unexpected feedback loop involving proteins usually found in different parts of the cell. More about that in just a moment. First, every story needs a setting.

The immune system — and countless other crucial biological functions — depends on complex biochemical chain reactions among proteins. These chain reactions are described by scientists as signaling pathways.

Wang and Duan are concerned with one pathway in particular, NF-κB (with the second-to-last character pronounced “kappa”). The pathway regulates important molecular interactions underlying both innate and adaptive immunity, as well as for a key function that causes defective cells to self-destruct. NF-κB is critical for human health, and excessive activation contributes to various disorders, including rheumatoid arthritis, atherosclerosis, inflammatory bowel diseases, multiple sclerosis and cancer.

“This might be one of the most important pathways in the whole field of immunology and biology,” Duan said.

The researchers detailed one set of reactions within the NF-κB pathway in a series of over two-dozen experiments with cells and laboratory models, meticulously following the evidence and ruling out alternative explanations for the phenomena they observed. Throughout, a common bacterial toxin was used to activate innate immune signaling.

The researchers started by identifying an enzyme, called USP3, that strongly suppresses NF-κB signaling.

Looking deeper, the team identified a sort of signaling middle-man affected most strongly by the enzyme, a protein called MyD88. After any one of multiple recognition proteins detects a bacterium, MyD88 is activated to transmit the alarm downstream. The set of reactions ultimately causes inflammatory molecules to be released. Importantly for the story, MyD88 must recruit other, smaller proteins that attach to it in order to relay its message.

Here’s where the story got strange: USP3’s home is in the cell nucleus. MyD88 does its work outside the nucleus, in the cytoplasm.

The researchers dug in to solve this mysterious connection, in part by labeling USP3 so that the enzymes light up when viewed through a microscope, then watching the live cells in real time. They showed that the initial encounter with the bacterial toxin caused USP3 to migrate out of the nucleus into the cytoplasm. There, the enzyme found MyD88 and cut off the extra proteins, effectively dampening its message. While most of the USP3 returned to the nucleus, some remained in the cytoplasm for more than two hours.

When the bacterial toxin was administered a second time after 12 hours, the USP3 remaining in the cytoplasm was available to snip MyD88 protein chains immediately. As a result, the cell’s response was suppressed compared to the first exposure — demonstrating that this piece of the innate immune system had learned to tolerate the toxin.

New avenues of bioscience and potential hints for treatment

These findings provide the first evidence that innate immune tolerance involves mechanisms that follow the translation of DNA into proteins. While this is expected to open new avenues of research far beyond Wang’s lab, the discovery also has implications for human health, given the host of illnesses caused by inflammation.

“In the early stage of infection, our innate immune response needs to be amplified to effectively fight it off,” Duan said. “But if this response persists or intensifies, it can lead to tissue damage, organ failure and even death from causes such as sepsis, which kills about 350,000 Americans each year. We found that USP3-mediated innate immune tolerance is a sophisticated and vital mechanism to prevent excessive NF-kB signaling and hyperinflammation leading to sepsis and other deadly conditions.”

The team is continuing to explore the molecular mechanisms that control innate immunity and provide its capacity to learn. They are exploring exactly how MyD88, and other messengers that build up longer protein chains, activate the NF-κB pathway. Other investigations aim to find out the duration USP3 hangs around in the cytoplasm after it’s initially deployed.

“Currently, we know this is a kind of short-term memory established by our body,” Duan said. “However, we want to know exactly how long this memory could last to protect us.”

About the study

In addition to Duan and Wang, the study’s other authors include Yang Du, Changsheng Xing, Junjun Chu, Xin Liu, Motao Zhu, Chen Qian, Bingnan Yin and Helen Y Wang from Keck School of Medicine of USC, and Yanchun Feng, Jiayu Ou and Jun Cui from the School of Life Sciences, Sun Yat‐sen University, Guangzhou China.

This work was partly supported by the National Key Basic Research Program of China (2020YFA0908700) and the National Natural Science Foundation of China (31870862) as well as by grants from the National Cancer Institute (NCI), National Institute of health (NIH) (R01CA101795 and R01CA246547), and Department of Defense (DoD) CDMRP BCRP (BC151081).

Learn more about bold research at the Keck School of Medicine of USC.