Immune cell map of pigs lung offers insights to improve human and animal health

• Researchers from the Babraham Institute and the Pirbright Institute have mapped the immune cell landscape of the pig lung and how this is impacted by immunological challenge.
• Their analysis reveals lasting immunological consequences of influenza infection and respiratory immunisation on the lung resident immune cells and adds depth to our knowledge of immune responses during respiratory infection and vaccination.
• This study is the first time pig lung cells from different immune contexts have been described in such detail and the data provides an atlas for future studies of immunity in the lung.

Research published today in PLOS Pathogens by scientists at the Babraham Institute and the Pirbright Institute provides important insights into the populations of cells that provide protection against respiratory pathogens. To better understand lung immunity, the team analysed individual cells from pig samples to generate an atlas that can be used to understand the difference between lung-resident and circulating immune cells following respiratory infection or vaccination. Understanding how an immune response is induced and maintained in the lung is crucial for the design of more effective vaccines to provide long-lasting immunity.

Influenza causes illness in both livestock and humans, and vaccination is a key means of controlling this pathogen. For a vaccine to provide the best protection, it is important that the right combination of immune cells and molecules are generated during the immune response. Humans and pigs share a similar anatomy and physiology; studies in pig are therefore a useful way to understand the immune system under controlled conditions for both species.

The immune responses to respiratory pathogens are initiated within the respiratory tract, where different cell populations act together to fight an infection. It is important for immunologists to look not only at cells from the blood, but also from the site of the infection, to ensure they have a full understanding of the characteristics of different cell populations during and after the immune response.

To create the atlas, the team looked at cells from pig lungs collected using a lung-washing technique (bronchoalveolar lavage) after influenza infection or vaccination and compared these to immune cells circulating in the blood. The samples were collected as part of another study and had been frozen to allow researchers to re-examine them as part of new research. Human lung washes to study immune responses have shown that examining lung cells in the context of respiratory diseases can tell us more than the analysis of cells from the blood.

The gene expression of a cell, called the transcriptome, provides information of cell type and activity. By applying single cell analysis of the transcriptome to the lung cells, the researchers were able to highlight differences between tissue resident and circulating immune cells, and the changes immune cell populations in the lung undergo during infection and immunisation. Together this detailed data can be visualised as an ‘atlas’ showing the overlap in properties of the cell populations and relationships between subsets. Drs Andrew Muir and Arianne Richard from the Babraham Institute performed the bioinformatic analyses in the study.

Dr Arianne Richard, group leader in the Babraham Institute’s Immunology research programme, said: “It is important to have a detailed picture of the immune cells found in tissues, compared to those circulating in the blood, especially in cases of respiratory viruses. Our atlas will be a useful resource for other immunologists looking at cell populations from sites of infection. Future research in this area will help us understand more about how cells in tissues contribute to the immune response and improve our defences against the global health threat of respiratory viruses.”

Previous research undertaken by the Pirbright Institute showed that pigs given a vaccine and IL-1β simultaneously did not show signs of protection against infection. IL-1β is a molecule that acts as an immune activator, and in mice, has been shown to enhance vaccine-mediated protection against influenza virus infection. To explore this finding in pigs more, the transcriptomic data analysed in this latest study found that IL-1β reduced the number of regulatory T cells, a type of immune cell that dampens immune response. Even though antibodies were generated to combat the virus, with fewer regulatory T cells, the scientists suggest that in pigs IL-1β leads to a dysregulated response and causes tissue damage instead of protection.

Dr Andrew Muir, postdoctoral researcher in the Richard lab who performed the bioinformatic analysis, said: “Our results show that vaccines, and the additional molecules that are added to them, can generate important differences in tissue resident cell biology. Learning more about the ways vaccine design influences tissue resident cells will serve as a foundation for being able to generate long term protection against respiratory viruses in pigs and potentially humans.”

The study also found increased expression of the protein IFI6 in the lung cells 21 days after infection, suggesting that antiviral activity in immune cells continues to persist for several weeks after the infection is gone. This shows that invading organisms can have a long-lasting impact on lung-resident immune cells.

Professor Elma Tchilian and Dr Wilhelm Gerner, heads of Mucosal Immunology and T-cell Biology Groups at the Pirbright Institute, said: “Our study allowed us to collect gene expression data which can act as a reference ‘atlas’ for future lung studies in pigs, an important model to study disease in humans and livestock.”