Researchers have produced an unusually detailed molecular map showing exactly how influenza A virus takes over human cells and disables their defenses, a discovery that could lead to better vaccines and antiviral drugs.
Scientists at EMBL Hamburg and the Leibniz Research Institute for Molecular Pharmacology developed a technique to watch protein interactions happening inside living, intact cells rather than in broken-apart samples. The breakthrough allowed them to see how viral proteins hijack human cellular machinery in real time, with enough precision to model how the invading proteins physically fit together with human proteins.
Influenza A causes 3 to 5 million severe infections worldwide each year and is responsible for up to 650,000 deaths. The virus has triggered multiple pandemics, including the 1918 Spanish Flu.
When influenza enters a cell, it releases RNA containing instructions for making viral proteins. Those proteins then spread through the host cell and redirect its molecular systems, transforming it into a factory for producing new virus particles.
The problem with old methods
For years, scientists studying flu-host interactions relied on breaking cells open to measure protein contacts. That approach had a critical flaw: the process distorts what was actually happening inside the living cell. Once internal compartments are destroyed, proteins that were separated in life come into contact in the lab. Meanwhile, weak or temporary interactions disappear, making it hard to know which connections truly existed during infection.
Researchers at FMP Berlin developed a specialized version of cross-linking mass spectrometry, a technique that captures protein-protein interactions directly inside intact, infected cells. The method can detect interactions that occur only briefly or in specific regions of the cell.
"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," said Boris Bogdanow, a Junior Research Group Leader at the Institute of Virology in Berlin. "This gives us insight into the interface between the virus and the human cell and may help identify actionable targets for future pharmaceutical interventions."
The researchers combined their experimental data with computational modeling using a modified version of AlphaFold, the Nobel prize-winning protein structure prediction algorithm. This allowed them to identify which viral and human proteins interact and estimate how those proteins are positioned when they connect.
Two ways the virus takes control
The study, published in Nature Microbiology, revealed two striking strategies influenza A uses to commandeer human cells.
The first involves hemagglutinin, a protein on the virus's surface that the virus uses to attach to and enter host cells. Researchers tracked this protein as it moved through the cell's internal transport network, which folds and modifies proteins before sending them to their final destinations. The analysis showed that several human proteins helped correctly fold and modify hemagglutinin during infection, with some of those host proteins having previously poorly understood functions.
The second discovery was unexpected. Influenza A infection caused paraspeckles, small droplet-like compartments in the cell nucleus, to dissolve. When these structures broke apart, they released RNA-binding proteins that had been contained inside them. The virus appears to commandeer those proteins to support its own replication.
"What surprised us most was the paraspeckles," said Iuliia Kotova, first author of the publication and now at ETH Zurich. "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."
The disruption may benefit the virus in multiple ways. Evidence suggests paraspeckles contribute to the cell's stress responses and antiviral gene regulation, so destroying them could weaken parts of the cell's natural defense system.
Jan Kosinski, Group Leader at EMBL Hamburg, noted that the work opens wider possibilities. "Our approach, combining in-cell cross-linking, structural modeling, and targeted cell-biology follow-up to map native virus-host interactions at specific stages of infection, remains broadly applicable," he said. "While the exact host factors and mechanisms often differ from virus to virus," the same strategy could eventually be used to investigate viruses with greater pandemic potential, such as H5N1.
Author Jessica Williams: "This is the kind of granular understanding that transforms how we build defenses against viral threats, and the methodology opens doors for studying far more dangerous strains."
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