Washington: Researchers at EMBL Hamburg and their collaborators have mapped, for the first time, how the influenza A virus directly rewires infected human cells by tracking virus-host protein interactions inside intact cells.

Published in Nature Microbiology, the peer-reviewed study offers unprecedented structural insight into how the virus hijacks cellular machinery, a breakthrough that could support the development of improved flu drugs and vaccines.

Seasonal influenza causes up to 650,000 deaths worldwide every year and leads to serious illness in an estimated 3-5 million people. Influenza A has also been responsible for several pandemics, including the 1918 Spanish Flu.

The research team from EMBL Hamburg, the Leibniz Research Institute for Molecular Pharmacology (FMP), Charite - Universitatsmedizin Berlin, and other collaborators used a customised experimental workflow to observe protein interactions directly inside infected human cells.

According to the researchers, this is the first large-scale map of direct virus-host protein contacts inside intact influenza-infected cells with sufficient structural detail to model how the proteins fit together.
"Our work provides a new way to study flu-host interactions in their native context and with structural insight," said Jan Kosinski, Group Leader at EMBL Hamburg and the Centre for Structural Systems Biology (CSSB), adding, "The current results are a snapshot of a moment during infection, and it opens the door to studying flu-host interactions across the entire infection cycle."

The researchers employed a specialised version of cross-linking mass spectrometry (XL-MS), adapted specifically for virus-infected cells, allowing them to capture short-lived and location-specific protein interactions that previous methods often missed.
"XL-MS allows us to capture protein-protein interactions directly in infected intact cells, while also providing structural information about how these interactions are happening," explained Boris Bogdanow, now a Junior Research Group Leader at the Institute of Virology, Charite - Universitatsmedizin Berlin, adding, "This gives us insight into the interface between the virus and the human cell and may, through structural modelling, help identify actionable targets for future pharmaceutical interventions."

The team combined XL-MS data with a modified version of AlphaFold, the protein structure prediction algorithm, to model how viral and human proteins physically interact.
"The key advantage of the modified AlphaFold approach is that it allowed us to feed our experimental cross-linking data directly into the structural modelling," Kosinski said, adding, "This tells the model which parts of the viral and host proteins are close to each other inside infected cells. This was especially useful for virus-host complexes, which are often difficult to predict reliably."

The study identified two major ways in which influenza A takes control of host cells. Researchers traced how the viral surface protein haemagglutinin moves through the cell's transport and processing system, revealing host proteins that assist the virus in folding and modifying this essential protein during infection.
The researchers also found that influenza A infection causes paraspeckles--small droplet-like compartments inside the cell nucleus, to dissolve, releasing RNA-binding proteins that the virus can use to replicate.
"What surprised us most was the paraspeckles," said Iuliia Kotova, first author of the study and currently at ETH Zurich, adding, "Watching these tiny organelles in the nucleus dissolve, consistently across every cell line and every flu strain we tested, told us this isn't a side effect of infection- it might be a strategy."
Kosinski added, "There may also be a second benefit for the virus: some evidence suggests paraspeckles contribute to cellular stress responses and antiviral gene regulation, so disrupting them could also weaken parts of the cell's defence response."

The study relied on shared scientific infrastructure across multiple institutions, including cross-linking mass spectrometry experiments at Charite in Berlin, glycoproteomics analyses at the EMBL Proteomics Core Facility, AlphaFold modelling on the EMBL Compute Cluster, and microscopy imaging at CSSB's Advanced Light and Fluorescence Microscopy Facility.

Looking ahead, the researchers believe the new approach could be applied to study other viruses beyond influenza.
"While the exact host factors and mechanisms often differ from virus to virus, we think our overall approach - combining in-cell cross-linking, structural modelling, and targeted cell-biology follow-up to map native virus-host interactions at specific stages of infection - remains broadly applicable," Kosinski said.
Bogdanow added, "Although this study has focused on a lab-adapted strain, this study lays the groundwork to apply the methodology to viruses of potential pandemic relevance, such as H5N1, and for uncovering the interaction networks that support their multiplication in human cells."

This report was published from a wire feed. Apart from the headline, the EdexLive Desk has not edited the copy.