When the groundbreaking geneticist Barbara McClintock was born in Hartford, Connecticut, in 1902, her parents initially named her Eleanor. But they soon felt that the name was too delicate for their daughter and began to call her Barbara instead, which they thought better suited her strong personality. Her parents accurately predicted her determination.
To say that McClintock was a pioneer is an understatement. In 1944, she became the third woman to be elected to the US National Academy of Sciences and the first woman to lead the Genetics Society of America. Shortly afterwards, she discovered that certain genetic regions in maize could jump around the chromosome and, consequently, influence the color of mottled ears of maize with kernels ranging from golden yellow to dark purple. She dubbed these jumping bits of genetic code “controlling units,” which later became known as transposons or transposable elements. Unfortunately, by the mid-1950s, McClintock began to sense that the scientific mainstream was not ready to accept her idea, and she stopped publishing her research into this area to avoid alienation from the scientific establishment. But scientific ideas can re-emerge and integrate into the mainstream, and 30 years later, McClintock received a Nobel Prize in Physiology or Medicine for her revolutionary insights into these moving chunks of genetic code.
In recent years, medical research has uncovered new evidence showing that moving parts of the genome in humans can contribute to life-threatening diseases ranging from cancer to diabetes. For example, a handful of hemophilia cases have been traced to transposable elements that, at some point before the patient was born, or even, perhaps, conceived, inserted themselves into and disrupted genes that facilitate blood clotting. At the same time, experiments also offer mounting data to suggest that some transposable elements—and the genes that these roving bits of DNA help to resurrect—have beneficial roles.
The study of transposable elements is a “hotbed of research,” according to Josh Meyer, a postdoctoral fellow who studies these bits of DNA at Oregon Health & Science University in Portland. “Way back in the mists of time for the field, the general category of these things was junk DNA,” he explains. Now, he says, researchers have begun to understand that transposable elements aren’t always neutral genetic components: “There’s nothing that transposon biologists love more than to have the discussion of whether these things are, on balance, bad for us or good for us.”
Since McClintock’s breakthrough, researchers have identified different classes of transposable elements in the genomes of every organism in which they have sought them, ranging from fruit flies to polar bears. About 3% of the human genome consists of transposons of DNA origin, which belong to the same class as the ones that McClintock studied in maize. The other type of transposable elements, known as retrotransposons, are more abundant in our genome. These include the transposable elements that originate from viruses and make up as much as 10% of the human genome1. These elements typically trace back many millennia. They arise when viruses integrate into the genome of sperm or egg cells, and thus get passed down from one generation to the next.
A-maize-ing insight: McClintock in 1947. Credit: Everett Collection Historical, Alamy
The ancient viruses that became ‘fossilized’ in the genome remain dormant for the most part, and degenerate over time. However, there are hints that they might have the ability to re-emerge and contribute to illnesses that some scientists say could include autoimmune disease and schizophrenia2. In one example, a 2015 study found elevated levels of one embedded virus, known as human endogenous retrovirus K, in the brains of individuals with amyotrophic lateral sclerosis, also known as Lou Gehrig’s disease3. However, researchers stress that the data do not yet establish a causal link.
Yet another category of retrotransposons, called long interspersed nuclear elements-1, or LINE-1 for short, make up a whopping 17% or more of the human genome4. When LINE-1 retrotransposons move within the genome of reproductive cells and insert themselves in new places, they can disrupt important genes. Researchers have so far identified more than 120 LINE-1 gene insertions, resulting in diseases ranging from muscular dystrophy to cystic fibrosis5.
Much of the focus on transposable elements—and particularly, on endogenous retroviruses and LINE-1s—has centered on the possible negative repercussions of these DNA insertions. But work tracing back to the 1980s has suggested that endogenous retroviruses may also support reproductive function in some way6. In 2000, scientists found that remnants of an ancient virus in the human genome encode a protein called syncytin, which cell experiments indicate is important for placental development7. And although it is not shown definitely, there are also hints that an endogenous retrovirus that became embedded in the DNA of a primate ancestor might help boost the production of the digestive enzyme amylase, which helps to break down starch, in our saliva8, 9.
To peer deeper into the effects of transposable elements in humans, geneticist Nels Elde and his colleagues at the University of Utah in Salt Lake City used CRISPR–Cas9 gene editing to target an endogenous retrovirus called MER41, thought to come from a virus that integrated into the genome perhaps as far back as 60 million years ago. The scientists removed the MER41 element from human cells cultured in a dish. In humans, MER41 appears near genes involved in responding to interferon, a signaling molecule that helps our immune response against pathogens. Notably, as compared with normal cells, cells engineered to lack MER41 were more susceptible to infection by the vaccinia virus, used to inoculate people against smallpox. The findings, reported last year, suggest that MER41 has a crucial role in triggering cells to launch an immune response against pathogens through the interferon pathway10.
Meyer stresses that these insights elevate the already eminent discoveries by McClintock. “I would hope she would be extremely gratified and vindicated,” he says. “She recognized a type of sort of factor of genomic dynamism that no one else had seen before. And I am firmly convinced that it’s going to only become more and more and more central to our understanding of how genomics works.”
In 2005, with a freshly minted doctorate in molecular genetics, Nels Elde landed a job as a research fellow in Seattle and was tasked with studying the evolution of the immune system of gibbons, a type of ape. Each morning as he biked to the lab downtown, he would pass the city’s zoo and hear its gibbons calling to each other. Occasionally, he would visit the zoo and look at them, but he had no idea at the time that the squirrel monkeys that he also saw there would feature so largely in his future research. At work, Elde’s primate investigations focused on the gibbon DNA that he was responsible for extracting and analyzing using sequencing machinery.
Then, six years ago, Elde received his first lab of his own to run, at the University of Utah. He did not expect his team’s first discovery there to come so swiftly, or that it would involve transposable elements. Elde had arrived at the university with the intention of learning how cells recognize and defeat invading viruses, such as HIV. But he hadn’t yet obtained the equipment that he needed to run experiments, despite already having two employees who were eager to do work, including his lab manager, Diane Downhour. Given the lack of lab tools, the two lab staff members spent their time on their computers, poking around databases for interesting patterns in DNA. After just two weeks of this, Downhour came into Elde’s office and told him that they had found a couple of extra copies of a particular gene in New World monkeys—specifically, in squirrel monkeys.
Elde initially brushed off Downhour’s insight. “I said, ‘Why don’t you go back to the lab and not worry about it?’” he recalls. But a couple of days later, she returned to his office with the idea. “I was just in the sort of panicked mode of opening a lab, ordering freezers, trying to set up equipment and hiring people,” Elde explains. “Diane definitely had to come back and say, ‘Come on, wake up here. Pay attention.’”
The gene that they detected multiple copies of in squirrel monkeys is called charged multivesicular body protein 3, or CHMP3. Each squirrel monkey seems to have three variants of the gene. By comparison, humans have only the one, original variant of CHMP3. The gene is thought to exist in multiple versions in the squirrel monkey genome thanks to transposable elements. At some point around 35 million years ago, in an ancestor of the squirrel monkey, LINE-1 retrotransposons are thought to have hopped out of the genome inside the cell nucleus and entered the cytoplasm of the cell. After associating with CHMP3 RNA in the cytoplasm, the transposable elements brought the code for CHMP3 back into the nucleus and reintegrated it into the genome. When the extra versions of CHMP3 were copied into the genome, they were not copied perfectly by the cellular machinery, and thus changes were introduced into the sequences. Upon a first look at the data, these imperfections seemed to render them nonfunctional ‘pseudogenes’. But as Elde’s team delved into the mystery of why squirrel monkeys had so many copies of CHMP3, an intriguing story emerged.
Hiding in plain sight: Squirrel monkeys carry extra copies of the CHMP3 gene. Credit: Ariadne Van Zandbergen, Alamy
The discovery of pseudogenes is not wholly uncommon. There are more than 500,000 LINE-1 retrotransposons in the human genome11, and these elements have scavenged and reinserted the codes for other proteins inside the cell as well. Unlike with the endogenous retroviral elements in the genome, which can be clearly traced back to ancient viruses, the origin of LINE-1 retrotransposons is murky. However, both types of transposable elements contain the code for an enzyme called reverse transcriptase, which theoretically enables them to reinsert genetic code into the genome in the cell nucleus. This enzyme is precisely what allowed LINE-1 activity to copy CHMP3 back into the genome of the squirrel-monkey ancestor.
Elde couldn’t stop thinking about the mystery of why squirrel monkeys had multiple variants of CHMP3. He knew that in humans, the functional variant of the CHMP3 gene makes a protein that HIV uses to bud off of the cell membrane and travel to and infect other cells of the body. A decade ago, a team of scientists used an engineered vector to prompt human cells in a dish to produce a truncated, inoperative version of the CHMP3 protein and showed that the truncated protein prevented HIV from budding off the cells12. There was hope that this insight would yield a new way of treating HIV infection and so prevent AIDS. Unfortunately, the protein also has a role in allowing other important molecular signals to facilitate the formation of packages that bud off of the cell membrane. As such, the broken CHMP3 protein that the scientists had coaxed the cells to produce soon caused the cells to die.
Given that viruses such as HIV use a budding pathway that relies on normal CHMP3 protein, Elde wondered whether the extra, altered CHMP3 copies that squirrel monkeys carry confers some protection against viruses at the cellular level. He coordinated with researchers around the globe, who sent squirrel-monkey blood from primate centers as far-reaching as Bastrop, Texas, to French Guiana. When Elde’s team analyzed the blood, they found that the squirrel monkeys actually produced one of the altered versions of CHMP3 they carry. This finding indicated that in this species, one of the CHMP3 copies was a functional pseudogene, making it more appropriately known as a ‘retrogene’. In a further experiment, Elde’s group used a genetic tool to coax human kidney cells in a dish to produce this retrogene version of CHMP3. They then allowed HIV to enter the cells, and found that the virus was dramatically less able to exit the cells, thereby stopping it in its tracks. By contrast, in cells that were not engineered to produce the retrogene, HIV was able to leave the cells, which means it could theoretically infect many more.
In a separate portion of the experiment Elde’s group demonstrated that whereas human cells tweaked to make the toxic, truncated version of CHMP3 (the kind originally engineered a decade ago) die, cells coaxed to make the squirrel-monkey retrogene version of CHMP3 can survive. And by conducting a further comparison with the truncated version, Elde found that the retrogene—what he calls retroCHMP3—in these small primates had somehow acquired mutations that resulted in a CHMP3 protein containing twenty amino acid changes. It’s some combination of these twenty points of difference in the protein made by the retrogene that he thinks makes it nontoxic to the cell itself but still able to sabotage HIV’s efforts to bud off of cells. Elde presented the findings, which he plans to publish, in February at the Keystone Symposia on Viral Immunity in New Mexico.
The idea that retroCHMP3 from squirrel monkeys can perhaps inhibit viruses such as HIV from spreading is interesting, says Michael Emerman, a virologist at the Fred Hutchinson Cancer Research Center. “Having an inhibitor of a process always helps you understand what’s important for it,” Emerman explains. He adds that it’s also noteworthy that retroCHMP3 wasn’t toxic to the cells, because this finding could inspire a new antiviral medicine: “It could help you to design small molecules or drugs that could specifically inhibit that part of the pathway that’s used by viruses rather than the part of the pathway used by host cells.”
Akiko Iwasaki, an immunologist at the Yale School of Medicine in New Haven, Connecticut, is also optimistic that the finding will yield progress. “What is so cool about this mechanism of HIV restriction is that HIV does not bind directly to retroCHMP3, making it more difficult for the virus to overcome the block imposed by retroCHMP3,” Iwasaki says. “Even though humans do not have a retroCHMP3 gene, by understanding how retroCHMP3 works in other primates, one can design strategies to mimic the activity of retroCHMP3 in human cells to block HIV replication.”
Elde hopes that, if the findings hold, cells from patients with HIV infection might one day be extracted and edited to contain copies of retroCHMP3, and then reintroduced into these patients. Scientists have already used a similar cell-editing approach in clinical trials to equip cells with a variant of another gene, called CCR5, that prevents HIV from entering cells. In these experiments, patients have received infusions of their own cells—modified to carry the rare CCR5 variant. But although preliminary results indicate that the approach is safe, there is not enough evidence yet about its efficacy. (Another point of concern is that people with the rare, modified version of the CCR5 gene might be as much as 13 times more susceptible to getting sick from West Nile virus than those with the normal version of this gene13.) By editing both retroCHMP3 and the version of CCR5 that prevents HIV entry into cells, Elde suggests, this combination of gene edits could provide a more powerful way of modifying patient cells to treat HIV infection.
“You could imagine doing a sort of cocktail genetic therapy in order to block HIV in a way that the virus can’t adapt around it,” Elde says. His team also plans to test whether retroCHMP3 has antiviral activity against other viruses, including Ebola.
Going retro: Human cells engineered to make retroCHMP3 (shown in green). Credit: Diane Downhour
The investigations into how pseudogenes and retrogenes might influence health are ongoing. And there is mounting evidence that the LINE-1 elements that create them are more active than previously thought. In 2015, for example, scientists at the Salk Institute in California reported a previously unidentified region of LINE-1 retrotransposons that are, in a way, supercharged. The region that the researchers identified encodes a protein that ultimately helps the retrotransposons to pick up bits of DNA in the cell cytoplasm to reinsert them into the genome14. The same region also enhances the ability of LINE-1 elements to jump around the genome and thus create variation, adding weight to the idea that these elements might have an underappreciated role in human evolution and in creating diversity among different populations of people.
The active function of transposable elements is more important than many people realize, according to John Coffin, a retrovirus researcher who divides his time between his work at the US National Cancer Institute in Frederick, Maryland, and Tufts University in Boston. “They can—and have—contributed in important ways to our biology,” he says. “I think their role in shaping our evolutionary history is underappreciated by many evolutionary biologists.”
On the move
Squirrel monkeys are not the only animals that might reap protection against viral invaders thanks in part to changes in the genome caused by transposable elements. In 2014, Japanese scientists reported on a chunk of Borna virus embedded in the genome of ground squirrels (Ictidomys tridecemlineatus). The team’s results from cellular experiments suggest that this transposed chunk encodes a protein that might interfere with the pathogenicity of external Borna viruses that try to invade these animals15. Humans also have embedded chunks of Borna virus in their genomes. But we don’t have the same antiviral version that the ground squirrels have—and we might therefore be less protected against invading Borna viruses.
Other studies of endogenous viruses might have clearer implications for human health, and so scientists are looking at the activity of these transposable elements in a wide range of other animals, including the house cat. This past October, another group of Japanese researchers found that viruses embedded in the genomes of domesticated cats have some capacity to replicate. This replication was dependent on how well the feline cells were able to squelch the endogenous viruses in the genome through a silencing process called methylation16. But perhaps the most striking example of a replicating endogenous retrovirus is in koalas. In the 1990s, veterinarians at Dreamworld, a theme park in Queensland, Australia, noticed that the koalas were getting lymphoma and other cancers at an alarming rate. The culprit turned out to be a retrovirus that was jumping around in the animals’ genomes and wreaking havoc. Notably, koalas in the south of the country showed no signs of the retrovirus, which suggests that the virus had only recently begun to integrate into these animals’ DNA17.
The risks of transposable elements to human health are a concern when it comes to the tissue transplants we receive from other species, such as from pigs, which have porcine endogenous retroviruses. These embedded viruses—which have the unfortunate abbreviation PERVs—can replicate and infect human cells.
Transplants from pigs, for example, commonly include tissues such as tendons, which are used in ACL-injury repair. But these tissues are stripped of the pig cells—and thus of PERVs—so that just the tissue scaffold remains. However, academic institutions and companies are actively designing new ways to use pig tissues in humans. Earlier this year, Smithfield Foods, a maker of bacon, hotdogs and sausages, announced it had launched a new bioscience unit to help supply pig parts to medical companies in the future. Meanwhile, George Church, a Harvard Medical School geneticist and entrepreneur, has formed a company called eGenesis Bio to develop humanized pigs for tissue transplantation. In March, the company announced that it had raised $38 million in venture funding. Church published a paper two years ago showing that his team had edited out key bits of 62 PERVs from pig embryos, disrupting the PERVs’ replication process and reducing their ability to infect human cells by 1,000-fold18.
Whereas Church and other scientists have tried disrupting endogenous retroviruses in animal genomes, researchers have also experimented with resurrecting them: a decade ago, a group of geneticists in France stirred up some controversy when the researchers recreated a human endogenous retrovirus by correcting the mutations that had rendered it silent in the genome for millennia. The scientists called it the ‘Phoenix’ virus, but it showed only a weak ability to infect human cells in the lab19. There was, perhaps unsurprisingly, pushback against the idea of resurrecting viruses embedded in our genome—no matter how wimpy the resulting viral creation.
But emerging data suggest that the retroviruses buried in the human genome might not be quite as dormant as we thought. The ability for these endogenous retroviruses to awaken from the genome “is more widespread than has been previously appreciated,” says virologist Renée Douville at the University of Winnipeg in Canada. She views this phenomenon as being the rule, rather than the exception within the cell: “These retroelements are produced from the genome as part of the cell’s normal function to varying degrees.”
A closer look: Nels Elde and Diane Downhour search genetic data in the lab. Credit: Julie Kiefer, University of Utah Health
Interestingly, the cellular machinery involved in keeping cancer at bay might also have a connection to transposable elements. One in three binding sites in the human genome for the important tumor-suppressor protein p53 are found within endogenous retroviruses in our DNA20. And last year, a team led by John Abrams at University of Texas Southwestern Medical Center in Dallas offered preliminary evidence that p53 might do its work by perhaps keeping embedded retroelements in check21.
“When I first started openly publicly talking about this story, some of my colleagues here who are in the cancer community said, ‘Hey, that’s cute, but it can’t be true. And the reason it can’t be true is that we would know this already,’” Abrams recalls. The reason it wasn’t seen before, he explains, is that many genetic analyses throw out repeated sequences—which often consist of retroelements. So his team had to go “dumpster diving” in the genetic databases for these sequences of interest to demonstrate the link to p53. Abrams suspects that when p53 fails to keep retrotransposons at bay, tumors might somehow arise: “The next question becomes, ‘How do you get to cancer?’” Abrams says that this is an example of what he calls “transposopathies.”
Not all scientists are convinced of a causal link between p53 and retroelements in cancer. “My question is, if p53 is so vital in suppressing retrotransposon activity in cancer, why do we not find evidence of dysregulated retrotransposons inserting copies of themselves into the tumor genome more often?” asks David Haussler, a genomics expert at the University of California, Santa Cruz. “Most tumors have p53 mutations, yet only a very small percentage of tumors show evidence of significantly dysregulated rates of new retrotransposon copy insertion.”
Still, there are others interested in exploring whether ancient viruses might reawaken in cancer or have some other role in this disease. Five years ago, scientists at the University of Texas MD Anderson Cancer Center reported that a type of viral protein produced by the human endogenous retrovirus type K (HERV-K) is often found on the surface of breast cancer cells. In a mouse experiment, they showed that cancers treated with antibodies against this protein grew to only one-third of the size of tumors that did not receive this therapy22.
But some cancer scientists are thinking about co-opting endogenous retroviruses to use against cancer. Paul Bieniasz of the Rockefeller University in New York City gained insight into this approach by studying human endogenous retrovirus type T (HERV-T)—an ancient virus that spread for 25 million years among our primate ancestors until its extinction roughly 11 million years ago and at some point became fossilized in our DNA lineage. In April, his group found that a particular HERV-T encodes a protein that blocks a protein called monocarboxylate transporter 1, which is abundant on the surface of certain types of cancer cells23. It’s thought that monocarboxylate transporter 1 has a role in enabling tumors to grow. Blocking it could help to stymie the expansion of malignancies, Bieniasz speculates. He and his colleagues are now trying to build an ‘oncolytic virus’ that uses elements of HERV-T to treat cancer.
The idea that new viruses might still be trying to creep into our genomes is a scary one, even if they don’t appear very effective at achieving this. One of the most recent to integrate into our genome in a way that it is passed down from generation to generation is human endogenous retrovirus type K113 (HERV-K133), which sits on chromosome 19. It’s found in only about one-third of people worldwide, most of whom are of African, Asian or Polynesian background. And researchers say that it could have integrated into the genome as recently as 200,000 years ago6.
Although experts remain skeptical that a virus will integrate into the human genome again anytime soon, other transposable elements, such as LINE-1s, continue to move around in our DNA. Meanwhile, the field that Barbara McClintock seeded more than half a century ago is growing quickly. John Abrams, who is studying retroelements, says that we’re only just beginning to understand how dynamic the genome is. He notes that only recently have people begun to appreciate how the ‘microbiome’ of bacteria living in our guts can influence our health. “We’re really an ecosystem,” Abrams says of the gut, “and the genome is the same way.” There is the host DNA—belonging to us—and the retro-elements it contains, he explains, and “there’s this sort of productive tension that exists between the two.”
This article is reproduced with permission and was first published on July 11, 2017.