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A surprising way the immune system remembers – without antibodies

Antibodies always get the credit, but new UChicago Pritzker Molecular Engineering research shows how one type of white blood cell helps the body remember – and fight – invaders

Antibodies, which recognize viruses and proteins that the body has encountered before, have long gotten most of the credit for giving the human immune system a memory.

Now, researchers at the University of Chicago Pritzker School of Molecular Engineering (UChicago PME) have discovered a new form of immune memory. Macrophages, a type of white blood cell, adjust their molecular signaling patterns immediately after an infection, the researchers found. This short-term memory changes how macrophages respond to subsequent infections and immune signals – sometimes giving the cells a type of tolerance that makes them less responsive, sometimes strengthening their immune response.

The new findings, published in Cell Systems, could eventually point toward new ways of controlling macrophage activity to treat infections or autoimmune diseases.

“It turns out that macrophages can turn up or down their responses based on what they’ve been exposed to,” said UChicago PME Prof. Savas Tay, senior author of the new work. “The better we understand how inflammatory signals are influencing cell states in this way, the better we can design new cell therapies that take advantage of these dials to control the immune system.”

Redefining immune memory

Andrew Wang
MD/PhD student and first author Andrew Wang.

The human immune system has two lines of defense: the innate immune system acts quickly and non-specifically to detect and fight infections; the slower adaptive immune response recognizes and targets specific pathogens.

“Classically, what distinguishes the innate immune response from the adaptive immune response is that it doesn’t adapt; it doesn’t have a memory of prior stimuli,” said Andrew Wang, a University of Chicago MD/PhD student and first author of the new paper.

However, some recent studies have hinted that macrophages – part of the innate immune system – might vary their responses. Wang, Tay, and their colleagues wanted to investigate whether macrophages did indeed change over time.

To study this, they tested the impact of 80 different conditions – varying doses of six different bacterial and viral molecules – on macrophage activity using a high-throughput microfluidics platform they had previously designed. The exposure to inflammatory signals, they showed, sometimes led to a “priming” effect, making macrophages more responsive to future threats. But in other cases, it led to tolerance, where macrophages respond more weakly or slowly to a second exposure.

“Our results really underscored the complexity of immune signaling,” said Wang. “There are a lot of things going on and they all have different effects.”

There were no clear trends between the type of virus or bacteria and how immune signaling was changed. But in general, higher doses and longer exposures of a pathogen increased tolerance – which could be an adaptation to prevent the immune system from being overactivated, Wang said. Shorter exposures or lower doses often led to priming, making macrophages ready to respond to threats more aggressively.

When the team isolated macrophages from a mouse with sepsis – widespread inflammation that can follow a severe infection – they discovered that the cells had weaker than usual immune responses. The observation helps explain why patients with sepsis can be vulnerable to secondary infection. It also suggests that turning up macrophage activity – or blocking this “tolerance” – could help treat sepsis.

Predicting immune response

The researchers next showed that when macrophages were exposed to inflammatory signals, their activity changed alongside shifts in how the key immune regulator nuclear factor kappa-B (NF-κB) was activated and moved into the nucleus over time. At the same time, the accessibility of certain DNA regions changed, altering how easily NF-κB and other regulatory proteins could bind and activate inflammatory genes.

By combining NF-κB signaling patterns and chromatin accessibility data, the team developed a machine-learning model that could predict how macrophages will respond to new inflammatory signals based on prior exposure.

“What we’re beginning to understand is how a pathogen can perturb a macrophage and push it toward a new steady state,” said Wang. “This gives us new insight into the complexity of inflammatory signaling, but also could have some practical implications.”

In the current study, the team only followed macrophages for about 12 hours. However, they speculate that the effects on the cells could last for days or weeks – more research is needed to be sure.

Citation: “Macrophage memory emerges from coordinated transcription factor and chromatin dynamics,” Wang et al., Cell Systems, February 11, 2025. DOI: 10.1016/j.cels.2025.101171

Funding: This work was supported by the University of Chicago Materials Research Science and Engineering Center, the National Science Foundation, and a Fulbright PhD student scholarship.