Tracking the flu into its first battlefield: the nose

The answer to fighting the flu could be right under our noses, or rather, inside them. New research details events in the nose during flu and could lead to new targets and more effective nasal flu vaccines.

The nose is often the gateway to respiratory infections, where viruses first take up residence and begin to replicate. But strangely, the immune response in the nose has been relatively unexplored.

“The National Heart, Lung, and Blood Institute has traditionally covered the lung through the trachea, and another NIH institute funds research for craniofacial and dental disorders,” says Boston Children’s Hospital researcher José Ordovás-Montañés, Ph .D. “Where does the nose fit?”

Ordovás-Montañés first took on this underfunded body part during the COVID-19 pandemic. His lab showed that people who developed severe COVID-19 had poor antiviral responses in the nose and throat. In a new study led by Samuel Kazer, Ph.D., the team looked at what happened in the noses of mice during influenza infection.

Unlike the COVID study, which looked at patients’ nasal swabs at one point in time, the new study tracked events across the entire nose, including the parts not accessible with a nasal swab, over the course of a flu episode.

To better understand immune memory, the researchers resampled the mice after a second flu infection. They published their findings in the journal Immunity.

An ‘atlas’ of cellular responses to influenza

Over the course of the infection, the researchers sequenced the RNA of thousands of individual cells in the nasal mucosa (the tissue that lines the nasal cavity)—a total of more than 150,000 reads over two weeks. This created a dynamic “atlas”, cataloging what types of cells were there and how each responded.

The team identified 127 types and subtypes of cells, including epithelial cells that line the mucosa, several types of immune cells, cells that form connective tissue, and even neurons that facilitate smell.

“We saw a lot of interesting cellular diversity in this micro-anatomy,” says Ordovás-Montañés. “When we sample people with swabs, we’re just scratching the surface. Sam was able to look at the whole tissue.”

Different cells came and went during influenza infection. For example, neutrophils (immune cells that respond first) appeared almost immediately, but left once the virus was cleared. Tissue-resident memory T cells (TRM cells), which maintain the memory of an infection in the tissue, appeared around day 14.

They remained in the nose afterward, even through the second bout of flu, as did the plasmablasts, which matured into antibody-producing plasma cells.

Keeping a memory of the flu

A previously undescribed group of cells entered the stage one to two weeks after infection began. Called Krt13+ nasal immune-interacting floor epithelial cells (KNIIFE cells), they run along the floor of the nasal cavity, just above the roof of the mouth. Kazer’s expertise at the intersection of biology and computational science made their discovery possible, says Ordovás-Montañés.

“I almost threw those cells away because they looked so weird,” he adds.

These cells may be the key to the faster, coordinated immune responses the team saw during the second flu infection.

“KNIIFE cells express many genes associated with immune function that we are not used to seeing in epithelial cells,” explains Kazer. “They expand after the virus is cleared, in the same anatomical location as the TRM cells. We think they can help preserve the memory of an infection.”

Pursuing to create a vaccine

The team is now further exploring the role of KNIIFE cells and plans to correlate the findings from the mice with nasal swab data from people with the flu and from children seen at Boston Children’s Hospital with other viral infections. Kazer hopes their work will one day lead to a long-lasting nasal vaccine that could limit the spread of the disease beyond the nose by helping the nose “remember” the flu virus.

“Memory can take place in many types of cells,” he says. “Understanding what memory looks like in a barrier tissue like the nasal mucosa is basic biology that we’re trying to get at.”