IFITM3 protein found to play critical role in restricting viral replication in vivo.

People who carry a particular variant of the interferon-inducible transmembrane 3 (IFITM3) gene are more likely to develop serious symptoms as a result of a flu virus infection than people who carry other variants of the gene, scientists report. An international team led by researchers at the Wellcome Trust Sanger Institute and Ragon Institute of Massachusetts General Hospital first demonstrated that mice lacking the Ifitm3 gene developed fulminant viral pneumonia when challenged with a normally mildly pathogenic influenza virus.

When the researchers then analyzed the IFITM3 alleles of patients who were hospitalized with seasonal or pandemic H1N1/09 virus, they found an increased frequency of a minor IFITM3 allele, SNP rs23352-C. Subsequent functional assays showed that the protein encoded by this IFITM3 gene variant was less capable of restricting influenza virus replication in vitro. The Sanger Institute’s Paul Kellam, Ph.D., and colleagues report their studies in Nature in a paper titled “IFITM3 restricts the morbidity and mortality associated with influenza.”

Recent in vitro studies have suggested that the IFITM protein family is involved in restricting replication of pathogenic viruses and is critical in terms of fundamental resistance to viruses such as influenza. The Sanger and Ragon Institute researchers tested the validity of these findings in vivo, by infecting IFITM3-deficient mice (Ifitm3-/-) with a low-pathogenicity murine-adapted H3N2 influenza A virus. These mice are homozygous for a mutated IFITM3 gene that isn’t translated into the IFITM3 protein.

While the influenza strain used to infect the animals doesn’t normally cause extensive viral replication throughout the lungs, the infected IFITM3-deficient animals lost over 25% of their body weight within just six days and exhibited symptoms of severe clinical illness. The virus also persisted for much longer in these mice than in infected wild-type littermates, and their lungs exhibited 10-fold higher levels of replicating virus.

When the team subsequently examined lung tissue from the IFITM3-/- mice,  they confirmed that viral infection had caused extensive edema and red blood cell estravasation as well as pneumonia, hemorrhagic pleural effusion, and multiple lesions on all lung lobes. All in all the pathology was similar to that produced by infection of mice and primates with the 1918 HINI virus strain.

Analysis of lung tissue cell populations in the IFITM3-/-  animals on day six post-infection showed a significant reduction in the proportions of CD4+ cells, CD8+ T cells, and natural killer (NK) cells  compared with wild-type infected mice and increased proportions of neutrophils. Moreover, despite extensive cellular infiltration, the absolute numbers of CD4+ T cells in the lungs of the IFITM3-/- mice were also lower than those in wild-type mice, and the numbers of neutrophils higher. These features were associated with exaggerated pro-inflammatory responses in the lungs of IFITM3-/-.

Interestingly, when IFITM3-/- and wild-type mice were challenged with an influenza strain that lacked the NS1 gene, which is primarily responsible for inhibiting the host’s natural immune responses, the animals were all equally able to fend off serious infection. “Unchecked lung viral replication and an enhanced inflammatory response accounts for the profoundly deleterious effects of viral infection in IFITM3-/- mice,” the authors conclude.

Moving on to test the relevance of their findings in humans, the team sequenced the IFITM3 gene in 53 patients who were hospitalized after infection with pandemic H1N1/09 or seasonal influenza virus. They found that there was significant over-representation of the synonymous SNP rs12252, which results in a change in the first splice acceptor site. This variant, the team suggests, may be associated with the IFITM3 splice variant ENST00000526811, which encodes a truncated IFITM3 protein lacking the first 21 amino acids.

Importantly, when the researchers tested the functional significance of the IFITM3 rs12252 polymorphism in vitro, they found that cells carrying the variant were more susceptible to infection and expressed much lower than normal levels of the IFITM3 protein.

They claim their findings in mice and humans demonstrate that IFITM3 expression represents an essential barrier to influenza A virus infection. “In effect, the host’s loss of a single immune effector, IFITM3, transforms a mild infection into one with remarkable severity,” they write. The authors stress that further study will be needed to pick apart how IFITM3 controls susceptibility to viral infections. “Our research is important for people who have this variant as we predict their immune defenses could be weakened to some virus infections,” Professor Kellan adds.

The findings also add more weight to the notion that the host’s genetic makeup as well as the strain of pathogen can influence how individuals fend off infections. “This important research adds to the growing scientific understanding that genetic factors affect the course of disease in more than one way,” remarks Sir Mark Walport, Wellcome Trust director. “Genetic variations in a virus can increase its virulence, but genetic variation in that virus’s host—us—matters greatly as well.” 

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