Virus News: University Of Colorado Researcher Says Ancient Parasites Shaped Human Responses To Current SARS-CoV-2 Virus

Virus News: A frequent medical question since the last century has been why are some individuals more resilient to viruses than others? Possible answers to that question has eluded researchers and scientists for centuries and, in the age of COVID-19, has come to represent one of the holy grails of biomedical research.


 
Dr Ed Chuong, an assistant professor of molecular, cellular and developmental biology at University of Colorado-Boulder, proposes an intriguing answer: Exposure to ancient parasites by our ancestors forever altered our genome, shaping the varied responses of our immune systems today.
 
Dr Chuong, who was awarded the prestigious $875,000 Packard Fellowship to explore the idea told media, "If you look closely at our genome, viruses have been shaping not only our lives but also our biology and evolution for hundreds of millions of years.”
 
He added, "It's possible that ancient viral sequences from past pandemics are now lending a hand in helping us fight modern ones."
 
To most people the word genome conjures images of the 20,000 genes that encode the proteins necessary for life. But in reality, notes Dr Chuong, we may be more virus than human.
 
Interestingly at least half the human genome is made up bits of DNA left behind by viruses and other virus-like parasites, known as transposons, which slipped into cells of our primate ancestors over the past 50 million years.
 
In detailed analysis of the human genome we can see traces of these invasions everywhere, like a fossil record of infections.
 
Significantly among those invaders were so-called endogenous retroviruses.
 
Just as viruses do, they behaved selfishly at first, coaxing their host cells to make more copies so they could rip through the body and infect others. Over time, they lost their ability to sicken and spread, but infiltrated germ cells like sperm or eggs baking their genetic recipe into generations to come.
 
Researchers have long assumed those remnants were useless "junk DNA."
 
However Dr Chuong and others have discovered that, in some cases, they were co-opted by mammalian hosts for evolutionary gain, influencing everything from cognition to reproduction to immune response.
 
Importantly one landmark study, scientists discovered a protein called Syncytin, derived from an endogenous retrovirus, which made the development of human placental tissue possible.
https://rep.bioscientifica.com/view/journals/rep/152/5/R167.xml
https://pubmed.ncbi.nlm.nih.gov/22381536/
https://pubmed.ncbi.nlm.nih.gov/18650494/
 
Dr Chuong's own follow-up research, published in the journal Nature Genetics, found that endogenous retroviruses also serve as on-off switches for gene networks that influence placental development. https://www.nature.com/articles/ng.2553
 
Dr Ch uong added, "The development of the placenta enabled live birth in mammals and was a major step in the evolution of our species and these ancient viruses played a key role.”
 
In that study, Dr Chuong said, “The mammalian placenta is remarkably distinct between species, suggesting a history of rapid evolutionary diversification. To gain insight into the molecular drivers of placental evolution, we compared biochemically predicted enhancers in mouse and rat trophoblast stem cells (TSCs) and found that species-specific enhancers are highly enriched for endogenous retroviruses (ERVs) on a genome-wide level. One of these ERV families, RLTR13D5, contributes hundreds of mouse-specific histone H3 lysine 4 monomethylation (H3K4me1)- and histone H3 lysine 27 acetylation (H3K27ac)-defined enhancers that functionally bind Cdx2, Eomes and Elf5—core factors that define the TSC regulatory network. Furthermore, we show that RLTR13D5 is capable of driving gene expression in rat placental cells. Analysis in other tissues shows that species-specific ERV enhancer activity is generally restricted to hypomethylated tissues, suggesting that tissues permissive for ERV activity gain access to an otherwise silenced source of regulatory variation. Overall, our results implicate ERV enhancer co-option as a mechanism underlying the extensive evolutionary diversification of placental development.”
 
Dr Chuong has since shifted his attention to the immune system, showing in 2016 that ancient viruses helped shape the interferon response ie the cellular alarm system that sounds within hours of infection.
 
He added, "We found fragments of old viruses that normally lay silent but turn on during infection, and when they do, they turn on nearby immune genes. Notably, when those viral fossils are removed and the cell is then infected, the immune response is muted.Our study was one of the first demonstrations of an ancient virus being co-opted for host defense and now necessary to fight modern viruses.”
 
Dr Chuong was working under stay-at-home orders early in the pandemic when he began to think more about why different people respond to infection, including SARS-CoV-2, differently.
 
Dr Chuong wondered: Could these ancient retroviruses provide another hidden layer of explanation?
He wrote a grant proposal centered around that question.The David and Lucile Packard Foundation named him among 20 early-career scientists across the nation to receive their award.
 
Dr Frances Arnold, chair of the Packard Fellowships Advisory Panel, in a statement,"In a year when we are confronted by the devastating impacts of a global pandemic, racial injustice and climate change, these 20 scientists and engineers offer us a ray of hope for the future."
 
Dr Chuong suspects that ancient parasites could be influencing human immunity today in one of two ways: Either different populations were exposed to different viruses in their evolutionary history, leaving them with different cellular machinery with which to fight off new threats; or they share the same bits of ancient DNA but much newer influences (in utero or in the environment) have silenced or awakened that immune machinery in ways that make some resilient and others vulnerable.
 
In order to learn more, he and his team will amass population-wide datasets of immune cells from humans and other mammals and apply high-powered computing techniques to sequence their genome, looking not only at genes present but also at transposons.
 
Although the science  in this area is young, Chuong hopes that it ultimately could lead to new diagnostic tests or even new treatments.
 
Dr Chuong said. "Learning how and why immune responses vary within a population could transform our ability to predict individual responses to infection and autoimmune diseases. To get this kind of recognition that these ideas are worth pursuing is incredible."
 
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