SPP1+ Microglia Are Associated with Neuroimmune Rewiring and Glutamatergic Neuronal Injury in ART-Suppressed People Living with HIV

For decades, the medical world celebrated a monumental victory against HIV: the development of antiretroviral therapy. These drugs are so effective that they can suppress the virus to undetectable levels in the blood, allowing people living with HIV to live long, healthy lives. However, a shadow remains. The virus does not disappear; it hides in a few specific cells, forming a "reservoir" that the drugs cannot reach. While the blood is clear, these hidden pockets of virus persist, waiting to reactivate if treatment stops. For a long time, scientists believed this reservoir was primarily a problem for the immune system in the rest of the body. But a growing body of evidence suggests the brain is a different story. The brain is a protected sanctuary, shielded by a tight barrier that keeps many drugs out. Inside, a special type of immune cell called a microglia acts as the brain's security guard, constantly patrolling for trouble. The critical question has been: does this virus hide in the brain's security guards, and if so, does it cause damage even when the patient is on successful treatment?

A new study by researchers at the University of North Carolina and the University of California, San Diego, has answered these questions with startling clarity. By examining brain tissue from people who died while on effective HIV treatment, the team discovered that the virus is indeed hiding in the brain's microglia. More importantly, they found that these infected cells are not just sitting quietly; they are actively reprogramming the brain's environment, causing inflammation and damaging neurons even though the virus is suppressed in the blood. The researchers identified a specific group of these infected cells that act as a persistent source of trouble, driving a cycle of injury that explains why some people continue to experience cognitive decline despite taking their medication.

To understand what was happening, the scientists looked at brain tissue from three groups of people: those who were never infected, those with active, uncontrolled HIV, and those who had been on suppressive therapy for a long time. They used advanced techniques to read the genetic instructions inside individual cells, essentially taking a census of every cell type in the brain and listening to what genes they were turning on or off. What they found was a dramatic shift in the brain's immune landscape. In people with active HIV, the brain was flooded with activated immune cells. But even in those on successful treatment, a specific type of activated microglia did not go away. In fact, this specific group of cells had grown nearly six times larger in treated individuals compared to uninfected people. These cells were not just present; they were the primary home for the hidden virus.

The researchers discovered that these persistent, infected microglia were speaking a different language than healthy cells. They were producing high levels of a protein called osteopontin, which acts as a distress signal. In a healthy brain, microglia communicate gently to maintain balance. In these treated brains, the infected cells were broadcasting loud, inflammatory signals that disrupted the normal conversation between immune cells and neurons. They were sending out messages that triggered a chain reaction, causing the brain's immune system to start "eating" the connections between neurons. This process, known as synaptic pruning, is a normal part of brain development, but when it goes into overdrive, it destroys the very pathways needed for thinking and memory.

One of the most striking findings was how these infected cells managed to survive the body's immune defenses. Normally, when a cell is infected, it displays a flag on its surface to tell the immune system, "I am sick, please destroy me." The study showed that the HIV-infected microglia in the brain were using a clever trick to hide. They were producing a viral protein called Nef, which acts like a pair of scissors, cutting off the display of these flags. This allowed the infected cells to remain invisible to the immune system while continuing to churn out inflammatory signals. It was a state of "immune evasion," where the virus stayed hidden inside the cell, but the cell itself remained a source of chronic irritation for the surrounding brain tissue.

This chronic irritation had a direct and devastating impact on the neurons. The study found that the inflammatory signals from these hidden reservoirs were causing severe stress to the brain's nerve cells. Specifically, the researchers observed a breakdown in the DNA repair mechanisms of the neurons. When DNA is damaged, cells usually have a way to fix it, but in these brains, that repair system was failing. As a result, the neurons began to die off. The researchers measured the loss of two critical types of neurons: those that excite the brain (glutamatergic) and those that calm it down (GABAergic). Even in people who had been on treatment for years, the number of these neurons remained significantly lower than in uninfected individuals. The brain had not recovered its full population of nerve cells, leaving a permanent gap in the network.

The researchers also tested whether this damage was caused directly by the virus or by the body's own response to it. They took healthy microglia from people without HIV and exposed them to interferon, a signaling molecule that mimics the body's response to a viral infection. Within days, these healthy cells began to look and act exactly like the infected cells found in the brains of people on treatment. They turned on the same inflammatory genes, started hiding their flags, and began to produce the same damaging signals. This confirmed that the problem was not just the presence of the virus, but the specific way the brain's immune system was reacting to it—a reaction that had become stuck in a loop, unable to shut off even after the virus was suppressed.

The study also looked at the specific genetic instructions the virus was using while it hid. In people with active, uncontrolled HIV, the virus was making many different parts of itself. But in the brains of people on treatment, the virus was mostly silent, producing only one specific piece of its genetic code: the instructions for the Nef protein. This suggests that the virus had entered a low-power mode, just enough to keep its hiding spot safe and maintain its ability to evade the immune system, but not enough to make new copies of itself. This minimal activity was sufficient to keep the Nef protein flowing, which in turn kept the immune evasion and inflammation going.

The implications of these findings are profound. For years, the goal of HIV research has been to find a cure that eliminates the reservoir. This study suggests that simply suppressing the virus in the blood is not enough to heal the brain. The reservoir in the brain is not a dormant sleeper; it is an active participant in a pathological process that continues to damage the brain long after the virus is controlled. The specific group of cells identified in this study, the ones producing osteopontin and hiding the virus, appear to be the key drivers of this ongoing injury. They are the source of the noise that drowns out the brain's natural ability to repair itself.

The researchers did not stop at identifying the problem; they also pointed toward a potential path forward. By mapping the exact signals these cells use to communicate and damage the brain, they have identified new targets for therapy. If scientists can find a way to block the osteopontin signal or stop the Nef protein from hiding the infected cells, it might be possible to break the cycle of inflammation. This could allow the brain to finally clear out the reservoir and, perhaps more importantly, stop the ongoing damage to neurons. The study does not claim to have solved the problem of HIV-associated cognitive decline, but it has provided a clear map of where the trouble lies. It shows that the battle for a cure must extend beyond the blood and into the brain, targeting the specific cells that have learned to hide in plain sight while quietly dismantling the mind.