Supplementing a vaccine with a substance that enhances immune responses could provide protection against a broad range of viruses, according to a study led by researchers at the Stanford University School of Medicine.
The vaccine-enhancing substance, known as an adjuvant, is AS03 — an oily chemical that contains vitamin E. When healthy participants were immunized with the H5N1 bird flu vaccine that included AS03, some cells of the innate immune system, an evolutionarily ancient system of defense, underwent sweeping epigenetic changes — chemical changes that do not modify the DNA sequence but can alter gene activity. This epigenetic reprogramming was associated with an elevated expression of antiviral genes and heightened resistance to Zika and Dengue viruses. By contrast, vaccination with either an H5N1 vaccine lacking AS03 or with the seasonal flu vaccine, which does not contain AS03, did not result in epigenetic changes that increased antiviral defense.
“This paper describes the discovery of a new way of turbocharging the innate immune system of humans, to imprint a heightened and broad resistance against any virus that could emerge in the future,” said Bali Pulendran, PhD, the Violetta L. Horton Professor II and professor of pathology and of microbiology and immunology. “Importantly, the results show that the turbocharging of the immune system can last for several weeks, perhaps even months.”
Striking the right balance, epigenetically
Previous research has shown that the Bacillus Calmette-Guérin vaccine against tuberculosis induces epigenetic changes in certain immune cells. But the extent to which other vaccines produce this effect has been an open question. What’s been missing is a comprehensive assessment of epigenetic changes during an immune response in humans, particularly at the single-cell level.
To address this knowledge gap, Pulendran and his team used a variety of cutting-edge genomics and systems biology tools to track how seasonal and pandemic influenza vaccination in humans changes the epigenetic landscape at the single-cell level. The researchers immunized 21 healthy adults with a trivalent inactivated seasonal influenza vaccine, or TIV, which protects against the H1N1 and H3N2 subtypes of influenza A viruses, as well as one influenza B strain. They also vaccinated additional healthy adults with an inactivated H5N1 vaccine, either with or without AS03, and gave them a booster shot three weeks later.
The TIV vaccine induced widespread, persistent epigenetic remodeling in innate immune cells, leading to diminished production of certain molecules called cytokines, which, when produced in excess, can cause enhanced inflammation that damages various tissues in the body during infections. Similar effects were observed in response to immunization with the AS03-adjuvanted H5N1 vaccine. The changes were most pronounced three to four weeks after vaccination, but traces of an altered epigenetic landscape were still detectable as late as six months after vaccination. Surprisingly, however, the AS03-adjuvanted H5N1 vaccine, but not TIV, also induced epigenetic remodeling in innate immune cells that led to enhanced vigilance to other viruses. The researchers collected blood samples at various time points from participants who received this vaccine, and then infected their immune cells with the Dengue or Zika virus. Compared with pre-vaccination levels, the concentration of these viruses in the cells was lower between three and six weeks after vaccination. The drop in viral levels was associated with vaccine-induced epigenetic changes that increased the activity of antiviral genes.
Taken together, the results show that the AS03-adjuvanted H5N1 vaccine can trigger two distinct types of epigenetic changes. The refractory state is characterized by impaired cytokine responses and is driven by activator protein 1, and the viral vigilant state enhances control over a broad range of viruses and is largely mediated by proteins called interferon response factors. Both the refractory state and the antiviral state can occur simultaneously, even in the same cell. “While seemingly paradoxical, this superimposition might represent an evolutionary adaptation to avoid excess inflammatory host damage during late stages of infections, while maintaining a state of immunological vigilance against viral infections,” Pulendran said.
Harnessing innate immunity for pandemic preparation
Beyond highlighting the potential benefits of including AS03 in TIV and other vaccines, the study sheds new light on the impressive capabilities of the innate immune system, which powered the wide-ranging, durable benefits of the AS03-adjuvanted H5N1 vaccine.
The innate immune system, which is present at birth, is the first line of defense against invading pathogens, offering protection within minutes or hours. By contrast, the adaptive immune system is slower to respond to a new pathogen, taking week or so before the responses are effective. But this type of immunity retains long-lasting memories of previous encounters with specific pathogens and destroys them when they attack again.
“What was surprising about our results was that the response of the innate immune system to vaccines or pathogens is thought be relatively short-lived, typically lasting a few days, perhaps a week or so, unlike the adaptive immune system, which can last for years or decades,” Pulendran explained. “In this paper, we show that vaccination can cause an epigenetic imprint and altered functional response in innate immune cells that can last for several weeks.”
AS03 now is being developed for COVID-19 vaccines based on an earlier study by Pulendran’s team in which they demonstrated that a vaccine with AS03 produced a long-lasting, protective immune response against SARS-CoV-2 in monkeys.
What remains unclear is how vaccination induces such persistent epigenetic changes in innate immune cells, including monocytes and myeloid dendritic cells, given that these cell types turn over in less than one week. In addition to exploring this question, Pulendran and his team plan to test whether epigenetic reprogramming mediates antiviral protection against distinct viruses in animals. They also aim to examine whether other vaccines and adjuvants produce effects similar to the AS03-adjuvanted H5N1 vaccine in humans.
The team’s research could have important implications for the design of vaccines with adjuvants that provide broad protection by manipulating the epigenetic landscape. “In particular, one could imagine such a strategy being used early on in a pandemic when conventional vaccines are not yet available,” Pulendran said. “These epigenetic adjuvants could be stockpiled for use against any pandemic that could emerge in the future, and deployed very early at the start of a pandemic, perhaps as a pill or a nasal spray, to imprint heightened antiviral resistance in the population.”
He added, “Just imagine, for example, back in January 2020 — when we were initially hearing about the first cases of COVID-19 from Wuhan — if we could have obtained a prescription for an epigenetic adjuvant from our doctor, driven to a local pharmacy and obtained a nasal spray that would have increased our resistance to any virus. Just think how many people could have been saved.”
Other Stanford co-authors are Paul Utz, MD, professor of medicine; Purvesh Khatri, PhD, associate professor of medicine and of biomedical data science, Alex Kuo, PhD, basic life science research scientist; former postdoctoral scholars Thomas Hagan, PhD, and Sanne De Jong, PhD; Michele Donato, PhD, senior data scientist; postdoctoral scholars Peggie Cheung, PhD, and Chunfeng Li, PhD; graduate student Mai Dvorak; former life science research professionals Mariko Hinton Foecke and Sarah Chang, MS; Holden Maecker, PhD, professor of microbiology and immunology; Mario Cortese, PhD, former research scientist; and Mark Davis, PhD, director of the Stanford Institute for Immunity, Transplantation and Infection, the Burt and Marion Avery Family Professor, and professor of microbiology and immunology.
Researchers from the University of California, Berkeley; University of California, San Diego; GlaxoSmithKline; Emory University School of Medicine; and Chan-Zuckerberg Biohub also contributed to the study.
The work was supported by the National Institutes of Health (grants HIPC 4U19AI090023-11 and CCIH 5U19AI057266-17), Open Philanthropy and GlaxoSmithKline Biologicals SA.