Mapping immune cell response to Venezuelan equine encephalitis virus

Researchers in Lawrence Livermore National Laboratory’s (LLNL) Bioscience and Biotechnology Division have made significant progress in understanding how our immune systems respond to the Venezuelan equine encephalitis virus (VEEV), a highly infectious pathogen and weaponizable biothreat that causes neurological disease in humans.

The research, published in Frontiers in Immunology and funded by LLNL’s Laboratory Directed Research and Development program (22-ERD-038), provides a detailed map of how immune cells infiltrate the brain during VEEV infection, shedding light on the mechanisms that drive brain inflammation and offering clues for developing better treatments.

While immune cells are essential for fighting off viruses, they play a paradoxical role in VEEV infections, resulting in excessive inflammation in the brain that can lead to severe damage. To develop effective treatments, scientists need to understand which immune cells are involved, how they behave during infection and how they either protect or harm the brain.

Whereas previous research focused on the role of antibody-based therapeutics and their ability to clear VEEV from the body before it reaches the blood-brain barrier, this new study shifts the focus to what happens once the virus is in the brain.

In the latest study, scientists used advanced single-cell RNA sequencing and spatial transcriptomics—a technique that shows where genes are active in tissues—to track how individual immune cells respond to VEEV infection in the brain. This allowed the team to analyze the activity of immune cells at different stages of infection and map where these cells formed localized clusters in the brain, revealing patterns of immune cell infiltration.

The researchers focused on three key stages of infection: early infection, when the virus begins to replicate in the brain; peak viral replication and the onset of severe inflammation; and late-stage infection, when neurological symptoms like ataxia (loss of coordination) appear.

Microglia, the brain's resident immune cells, were the first to respond to VEEV infection. They transitioned from a "resting" state to an "activated" state, producing antiviral molecules like interferons and inflammatory cytokines. After microglia activation, large numbers of myeloid cells (monocytes and macrophages) infiltrated the brain, followed by natural killer (NK) cells and T cells.

Myeloid cells were found to cluster in specific regions of the brain, such as the hippocampus and the periphery of the cortex. This suggests that these cells may play a localized role in driving inflammation and damage. Both NK cells and T cells (specifically, CD8+ T cells) expressed high levels of cytotoxic molecules like perforin and granzyme B, which can kill infected cells but may also damage healthy brain tissue.

Altogether, this study provides a high-resolution, time-resolved analysis of immune cell activity in the brain during VEEV infection, putting researchers one step closer to developing effective treatments for viral encephalitis and other neuroinflammatory diseases.

LLNL coauthors of the study include Margarita Rangel, Aimy Sebastian, Nicole Leon, Ashlee Phillips, Bria Gorman, Nicholas Hum and Dina Weilhammer.

–Physical and Life Sciences Communications Team