A Single Genetic Variant Affects Immune Response to an Experimental Flu Vaccine

Date: August 10, 2022 By: Emily Makowski

Key Takeaways

  • A single genetic variant on human B cell receptors is responsible for differences in immune response to an experimental universal flu vaccine that targets the influenza viral spike protein.
  • Findings suggest some people may not have broadly neutralizing antibody responses to universal flu vaccines, but there is the potential to rescue immune response.

BOSTON – The influenza virus is constantly mutating, so influenza vaccines need to be updated from year to year and don’t provide broad protection against the virus. Research into a universal flu vaccine is a high priority in vaccine development. Previous work from researchers at the Ragon Institute of MGH, MIT and Harvard showed that the human gene IGHV1-69, which helps form the antigen binding surface of B cell receptors (BCRs), provides genetically-hardwired affinity for a site of vulnerability on flu, enabling ‘gene encoded’ broadly protective antibodies (bnAbs). Now, new research from the Ragon Institute and collaborators that builds upon this work has found that a subtle polymorphism, or gene difference, in the IGHV1-69 sequence can control the production of bnAbs elicited with an experimental universal flu vaccine.

In one approach to universal flu vaccine development, researchers have aimed to target specific regions of hemagglutinin, the spike protein of the influenza virus, which attaches to cells during infection. Hemagglutinin has a bulbous head region and a thin stalk region. Researchers have targeted the stalk because it is a conserved region—an area on the spike protein that doesn’t accumulate mutations as quickly as the head area. In 2019, researchers led by Daniel Lingwood, core member of the Ragon Institute of MGH, MIT and Harvard and associate professor of medicine at Harvard Medical School, published a paper in Immunity showing that an antibody produced by the human gene IGHV1-69 has natural affinity for the influenza virus’s hemagglutinin stalk. This genetically deterministic targeting by IGHV1-69 BCRs enabled vaccine-amplification of broadly neutralizing antibody responses to fight the virus. “This constitutes a gene-encoded pathway that can be triggered by universal vaccine concepts,” Lingwood says.

However, the gene has two different forms, or alleles. One of the alleles, called F54, causes the amino acid phenylalanine to be in the region of the B-cell receptor that targets the virus. The other form, L54, creates the amino acid leucine instead. In the new study, also published in Immunity, researchers wanted to know whether L54 could also support vaccine elicitation of broadly protective antibodies. They bred humanized mice, mice with human-like immune systems, that either had two copies of F54, two copies of L54, or one copy of each.

In human responses to flu, the vast majority of broadly protective responses to the influenza hemagglutinin stalk are dominated by the F54 allele. “About 80 percent, actually, of the response is F54. L54 is still used, but it’s used at a significantly lower frequency,” says Maya Sangesland, a postdoctoral fellow at the National Institute of Allergy and Infectious Diseases’ Vaccine Research Center, who completed the research while a graduate student at the Ragon Institute.

This could be a problem for humans who have the L54 form of the gene because it suggests that a universal flu vaccine targeting hemagglutinin may not be effective. “Individuals that are homozygous for F54 will likely be able to generate a high-titer, broadly protective response using IGHV1-69, but people with the L54 version may not be able to do so. It may require personalized medicine or an alternative vaccine approach to vaccine-amplify these responses,” Sangesland says. About 13 percent of people worldwide have only L54; South Asians are more likely to be homozygous for this allele than people of other ethnic groups.

Using cryo-electron microscopy, the researchers first determined the structure of the antibodies generated by F54 and L54 to figure out why L54 is not as effective. “We looked at the atomic and molecular details. And when we went into these atomic details, it was revealed how these antibodies, through very small and subtle changes, made molecular contacts that allow us to know whether they are protective or not,” says Alba Torrents de la Peña, a postdoctoral fellow in Andrew Ward’s lab at the Scripps Research Institute who performed the structural biology research.

“It wasn’t for any reason that we might initially expect,” Lingwood says. L54 provided great chemical specificity for the target, but was associated with antibody autoreactivity, or targeting of ‘self’. In the humanized mouse system this triggered tolerance, immune responses that cleared L54 antibodies to protect the organism’s own cells and tissues and ultimately prevented vaccine-amplification of broadly protective antibodies against influenza virus.  “It is one of the few examples where we can actually demonstrate a functional consequence of a genetic polymorphism in an antibody gene and suggests a reason why the L54 form is disfavored in human responses against flu,” Lingwood says.

Importantly, the researchers were able to use antibody-based immune cell checkpoint inhibitors to dampen L54 autoreactivity and rescue the immune response in humanized mice, which suggests a potential clinical intervention for people who have the L54 allele. Researchers will continue to study this gene variation in order to better understand the possibilities for making improved flu vaccines.

This research was supported by NIH (DP2DA042422, R01AI124378, R01AI153098, R01AI155447, U19AI057229, and P30AI060354), the Harvard University Milton Award, the Gilead Research Scholars Program, the NSF Graduate Research Fellowship Program, and NIH fellowship (F31Al138368).

About the Ragon Institute

The Ragon Institute of MGH, MIT and Harvard was established in 2009 with a gift from the Phillip T. and Susan M. Ragon Foundation, with a collaborative scientific mission among these institutions to harness the immune system to combat and cure human diseases. Focusing on global infectious diseases, the Ragon Institute draws scientists, clinicians and engineers from diverse backgrounds and areas of expertise to study and understand the immune system with the goal of benefiting patients. For more information, visit www.ragoninstitute.org.

About the Massachusetts General Hospital

Massachusetts General Hospital, founded in 1811, is the original and largest teaching hospital of Harvard Medical School. The Mass General Research Institute conducts the largest hospital-based research program in the nation, with annual research operations of more than $1 billion and comprises more than 9,500 researchers working across more than 30 institutes, centers and departments. In August 2021, Mass General was named #5 in the U.S. News & World Report list of “America’s Best Hospitals.” MGH is a founding member of the Mass General Brigham health care system.

Media contact: Emily Makowski, 716-598-0027, emakowski@mgh.harvard.edu

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