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Flu Virus Interaction with Host Cell Machinery Mapped Inside Infected Cells

Flu Virus Interaction with Host Cell Machinery Mapped Inside Infected Cells

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Researchers at EMBL Hamburg and collaborators at the Leibniz Research Institute for Molecular Pharmacology (FMP) have mapped in unprecedented detail how the influenza A virus (AIV) rewires infected human cells. The researchers developed a customized experimental workflow that used in-cell cross-linking mass spectrometry (XL-MS), combined with AlphaFold-based structural modeling and functional assays, to directly map protein-protein interactions (PPIs) in IAV-infected human cells.

They claim that the study marks the first time that scientists have mapped direct virus-host protein contacts at scale inside intact influenza-infected cells, with enough 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, PhD, group leader at EMBL Hamburg and the Centre for Structural Systems Biology (CSSB). “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.”

Kosinski is co-senior and co-corresponding author of the team’s published paper in Nature Microbiology, titled “Mapping in-cell protein contact sites reveals hijacking of paraspeckles during influenza A virus infection,” stating that their findings “… uncover mechanisms by which IAV exploits and remodels host compartments during infection.”

Every year, seasonal influenza kills up to 650,000 people globally and causes serious illness for 3–5 million individuals. When IAV infects cells, it releases RNA that contains the blueprints for a handful of proteins that spread throughout the host cell and repurpose its molecular machinery to make more viruses. “Its replication relies on protein–protein interactions (PPIs) between up to 14 viral proteins and host factors, often confined to cellular compartments and organelles,” the team stated.

Scientists want to understand this process in detail, as it would help in designing better drug therapies and vaccines against the flu virus. “Understanding these host–IAV PPIs in context is essential for elucidating viral strategies and therapeutic targets,” they added.

Studying protein-protein interactions in action during infection is challenging. Most previous studies relied on biochemical methods that required the cell to be broken open before the interactions could be measured. Once the cell’s compartments were gone, proteins that were never in contact inside the cell could meet in the test tube, and fragile or location-specific contacts could be lost. It was then hard to know which interactions actually happened inside an infected cell.

“This is when we learned that our collaborators—Boris Bogdanow and Fan Liu—at FMP Berlin had developed a specialized version of cross-linking mass spectrometry (XL-MS), a long-established technique for mapping protein contacts, tailored specifically to virus-infected cells,” said Kosinski. This was the critical breakthrough. It allowed researchers to do what previous methods couldn’t, including capturing short-lived and location-specific interactions.

“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 Bogdanow, who is now a junior research group leader at the Institute of Virology, Charité—Universitätsmedizin Berlin. “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.”

By combining the results obtained through XL-MS with computational structural modeling, the researchers could identify which viral and human proteins interact and also predict how they physically fit together. For this, they used a modified version of the protein structure prediction algorithm AlphaFold.

“The key advantage of the modified AlphaFold approach is that it allowed us to feed our experimental cross-linking data directly into the structural modeling,” explained Kosinski. “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 findings revealed two important ways in which the virus hijacks the cell. One involves hemagglutinin, a protein on the virus’s surface that it uses to bind and enter host cells. Tracing how hemagglutinin moves through the cell’s internal transport and processing system revealed how host proteins, some with previously unknown functions, helped the virus correctly fold and modify hemagglutinin during infection.

The other involves paraspeckles, small droplet-like compartments in the nucleus. The researchers found that infection by the influenza A virus causes these organelles to dissolve, releasing the RNA-binding proteins bound within them, which the virus can then use to replicate. “We identified host factors linked to the maturation of distinct glycoforms of the viral surface glycoprotein haemagglutinin through the membrane-bound endoplasmic reticulum–Golgi system,” the scientists wrote in summary. “In the nucleus, we observed the progressive disassembly of paraspeckles (phase-separated membraneless compartments) across multiple cell lines.”

First author Iuliia Kotova, PhD, former predoctoral fellow at the Kosinski group at EMBL Hamburg, and currently at ETH, said, “What surprised us most was the paraspeckles. 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 defense response.”

The researchers believe that their “mapping in context” approach can be used to understand the mechanism of action of other viruses that act similarly. “While the exact host factors and mechanisms often differ from virus to virus, we think our overall 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,” Kosinski said.

Bogdanow further commented, “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.”

The post Flu Virus Interaction with Host Cell Machinery Mapped Inside Infected Cells appeared first on GEN – Genetic Engineering and Biotechnology News.

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De novo L-(+)-tartaric acid biosynthesis in multi-modular engineered yeasts

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Capricor CEO won’t rule out legal action against FDA after negative adcomm

Capricor CEO won’t rule out legal action against FDA after negative adcomm

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After an FDA advisory committee voted 9-3 on Wednesday against recommending Capricor Therapeutics’ Duchenne muscular dystrophy cardiomyopathy drug for approval, stakeholders allege an “ulterior motive” and “biased intentions.”​ ​Read More

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Ketamine Triggers Sex-Specific Brain Recovery Responses

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During ketamine anesthesia the brain’s nerve cells fall silent, and as consciousness returns, they begin to reconnect. A study in mice by researchers at the Institute of Science and Technology Austria (ISTA) and colleagues at Allen Institute for Brain Science in Seattle, has now for the first time shown that immune cells in the brain play a critical role in this process, and indicates that there are differences between female and male brains.

Senior and corresponding author Sandra Siegert, PhD, at ISTA, reported on their findings in Science Advances, in a paper titled “Corticosterone-linked microglial activity underpins sexually dimorphic neuroplasticity after ketamine anesthesia,” in which they concluded “Our study uncovers significant sex-specific differences in neuronal adaptation during recovery from ketamine anesthesia, driven by microglia.”

Recovery from anesthesia is critical for resuming normal physiological and neuronal functions, but the mechanisms involved remain elusive, the authors wrote. “Ketamine distinguishes itself from other anesthetics by its unique pharmacological properties as an N-methyl D-aspartate (NMDA) receptor antagonist, which preferentially targets GABAergic inhibitory interneurons.”

And unlike many other anesthetics, ketamine does more than induce unconsciousness. It alters how we perceive pain and form memories. It dampens communication between neurons—the very network that must later resume normal function as the patient awakens. Exactly how this recovery process unfolds—and whether male and female brains differ in this regard—has been unclear. “…  ketamine anesthesia induces mild anxiety behavior phenotypes, interestingly, only in females,” the team continued, “suggesting inherent sex differences in anesthesia recovery with neuronal consequences that extend beyond the immediate sex-dependent metabolic processing described for low-dose ketamine.”

Working with mice, Siegert, together with Alessandro Venturino, PhD, and their colleagues at ISTA, and researchers at the Allen Institute, now offer the first answers to some of these questions. Microglia are specialized immune cells that constantly scan the brain and, when needed, trigger anti‑inflammatory responses. They also monitor neurons and their connections, thus helping to maintain optimal brain function. “Ketamine, across different dosages, affects microglia, which are embedded within the neuronal network,” the team explained. “Locally, microglia influence the synaptic machinery and neuronal firing properties by responding to environmental changes.”

As early as 2017, Siegert’s group at ISTA noticed that male and female mice respond differently to ketamine anesthesia, and more precisely, their microglia do.

For the newly reported study, using a cranial window—a surgically implanted opening that allows microscopic access to the living brain—Venturino analyzed how microglia and neurons behave while mice recover from ketamine anesthesia. Both cell types were labeled with fluorescent markers to glow under the microscope.

The researchers observed microglia processes in their dynamic action towards neurons. Surprisingly, as female mice recovered from anesthesia, microglia began forming prolonged contacts with neurons, coinciding with the onset of synaptic remodeling and plasticity. Notably, this phenomenon was not observable in male mice.

Furthermore, in mice lacking microglia, no such synaptic remodeling occurred, indicating that microglia are critical mediators of this recovery-associated plasticity. “What was fascinating,” Venturino explains, “was that we observed this plasticity—the brain’s ability to change, adapt, and in this case recover—only in females.”

Despite many other projects—or perhaps because of them—the researchers kept returning to their initial observation. “I’ve always believed that women have greater brain plasticity,” Siegert said with a smile. “Alessandro and I just couldn’t let it go—we wanted to know why.”

Further experiments revealed that this plasticity depends on corticosterone, one of the major stress hormones. “During recovery from anesthesia, corticosterone levels rise,” Venturino explained. “In female mice, this specifically activates the stress‑response gene Fkbp5 in microglia. The gene encodes the protein FKBP51, which helps the cell manage stress signals—and apparently prompts microglia to interact with neurons.”

The authors further noted, “Mechanistically, we found that female microglia selectively up-regulated the cochaperone Fkbp5/FK506-binding protein 51 (FKBP51), which is a key intermediary in the corticosteroid-induced stress response … Our findings underscore that microglia serve as a relevant interface between the endocrine stress response and the brain -immune cell system.”

To confirm this link, the team removed the adrenal glands—the endocrine organs that produce corticosterone. Without them, the close contact between microglia and neurons during recovery disappeared. “These results clearly show that corticosterone triggers this reaction in female mice,” said Venturino.

Siegert added, “They also remind us that stress is not always harmful—stress hormones are essential for certain processes in the brain.” In their paper the investigators commented, “The selective hypothalamic activation and elevated blood plasma corticosterone levels during the recovery phase in females shape the microglia-neuron interactions, highlighting a link between the endocrine and the brain-immune axes.”

Why this process differs between female and male mice remains uncertain; it is still unclear whether the male brain uses a similar mechanism, just delayed, or has another strategy. “Microglia enable rapid adaptation, and these cells in females are likely more sensitive to specific stress signals,” Siegert noted.

From an evolutionary viewpoint, she speculates, females may have faced greater demands for social, emotional, and multitasking adaptability—for example, in childcare, food gathering, or coordinating group activities. The female brain, therefore, had to adapt and respond more swiftly. “That’s a good thing,” Siegert added “But if this plasticity becomes too frequent or too intense, it can increase the risk of depression. We also know that psychiatric disorders are more prevalent in women than in men.”

Siegert further pointed out that during the literature review, her team found very few studies in which ketamine had been tested in females. “There were only a handful of anecdotal studies showing that women experience nausea and sickness more often after ketamine anesthesia,” she stated. Given that ketamine is also used as an antidepressant, understanding how its mechanisms differ between the sexes is all the more important. “It’s astonishing how readily people assume that men and women respond to drugs in the same way—when clearly they do not,” Siegert stressed.

Research like this is a step in the right direction: it highlights that medications can act differently in women and men and serves as a call to consider sex‑specific differences in future studies. “Our findings contribute to a growing body of evidence recognizing sex-specific differences in brain function and immune responses, the latter of which is already well known for increased susceptibility to infection and autoimmune diseases,” the team pointed out. “Our results identified a link between microglia-specific Fkbp5 expression and ketamine action, warranting a reevaluation of assumptions that ketamine is a general anesthetic and fully reversible across sexes.”

Insights into the microglia response to ketamine have since inspired Siegert and Venturino to co‑found Syntropic Medical, a start‑up in ISTA’s XISTA ecosystem exploring how 60 Hz flickering light can soften such neural networks in the brain.

The post Ketamine Triggers Sex-Specific Brain Recovery Responses appeared first on GEN – Genetic Engineering and Biotechnology News.

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