The Women of RNA: Two Award-Winners Share Why They Spent Their Careers Studying DNA's Lesser-Known Cousin
Lina Zeldovich has written about science, medicine and technology for Popular Science, Smithsonian, National Geographic, Scientific American, Reader’s Digest, the New York Times and other major national and international publications. A Columbia J-School alumna, she has won several awards for her stories, including the ASJA Crisis Coverage Award for Covid reporting, and has been a contributing editor at Nautilus Magazine. In 2021, Zeldovich released her first book, The Other Dark Matter, published by the University of Chicago Press, about the science and business of turning waste into wealth and health. You can find her on http://linazeldovich.com/ and @linazeldovich.
When Lynne Maquat, who leads the Center for RNA Biology at the University of Rochester, became interested in the ribonucleic acid molecule in the 1970s, she was definitely in the minority. The same was true for Joan Steitz, now professor of molecular biophysics and biochemistry at Yale University, who began to study RNA a decade earlier in the 1960s.
"My first RNA experiment was a failure, because we didn't understand how things worked," Steitz recalls. In her first undergraduate experiment, she unwittingly used a lab preparation that destroyed the RNA. "Unknowingly, our preparation contained enzymes that degraded our RNA."
At the time, scientists pursuing genetic research tended to focus on DNA, or deoxyribonucleic acid — and for good reason. It was clear that the enigmatic double-helix ribbon held the answers to organisms' heredity, genetic traits, development, growth and aging. If scientists could decipher the secrets of DNA and understand how its genetic instructions translate into the body's functions in health and disease, they could develop treatments for all kinds of diseases. On the contrary, the prevailing dogma of the time viewed RNA as merely a helper that passively carried out DNA's genetic instructions for protein-making — so it received much less attention.
But Maquat and Steitz weren't interested in heredity. They studied biochemistry and biophysics, so they wanted to understand how RNA functioned on the molecular level — how it carried instructions, catalyzed reactions, and helped build protein bonds, among other things.
"I'm a mechanistic biochemist, so I like to know how things happen," Maquat says. "Once you understand the mechanism, you can think of how to solve problems." And so the quest to understand how RNA does its job became the focus of both women's careers.
"People can now appreciate why some of us studied RNA for such a long time."
Half a century later, in 2021, their RNA work has earned two prestigious recognitions only months from each other. In February, they received the Wolf Prize in Medicine, followed by the Warren Alpert Foundation Prize in May, awarded to scientists whose achievements led to prevention, cure or treatments of human diseases.
It was the development of the COVID-19 vaccines that made RNA a household name. Made by Moderna and Pfizer, the vaccines use the RNA molecule to deliver genetic instructions for making SARS-CoV-2's characteristic spike protein in our cells. The presence of this foreign-looking protein triggers the immune system to attack and remember the pathogen. As the vaccines reached the finish line, RNA took center stage, and it was Maquat's and Steitz's research that helped reveal how these molecular cogwheels drive many biological functions within cells.
If you think of a cell as a kingdom, the DNA plays the role of a queen. Like a monarch in a palace, DNA nestles inside the cell's nucleus issuing instructions needed for the cell to function. But no queen can successfully govern without her court, her messengers, and her soldiers, as well as other players that make her kingdom work. That's what RNAs do — they act as the DNA's vassals. They carry instructions for protein assembly, catalyze reactions and supervise many other processes to make sure the cellular kingdom performs as it should.
There are a myriad of these RNA vassals in our cells, and each type has its own specific task. There are messenger RNAs that deliver genetic instructions for protein synthesis from DNA to ribosomes, the cells' protein-making factories. There are ribosomal RNAs that help stitch together amino acids to make proteins. There are transfer RNAs that can bring amino acids to this protein synthesis machine, keeping it going. Then there are circular RNAs that act as sponges, absorbing proteins to help regulate the activity of genes. And that's only the tip of the iceberg when it comes to RNA diversity, researchers say.
"We know what the most abundant and important RNAs are doing," says Steitz. "But there are thousands of different ones, and we still don't have a full knowledge of them."
Critical to RNA's proper functioning is a process called splicing, in which a precursor mRNA is transformed into mature, fully-functional mRNA — a phenomenon that Steitz's work helped elucidate. The splicing process, which takes place in cellular assembly lines, involves removing extra RNA sequences and stringing the remaining RNA pieces together. Steitz found that tiny RNA particles called snRNPs are crucial to this process. They act as handy helpers, finding and removing errant genetic material from the mRNA molecules.
A dysfunctional RNA assembly line leads to diseases, including many cancers. For instance, Steitz found that people with Lupus — an autoimmune disorder — have antibodies that mistakenly attack the little snRNP helpers. She also discovered that when snRNPs don't do their job properly, they can cause what scientists call mis-splicing, producing defective mRNAs.
Fortunately, cells have a built-in quality-control process that can spot and correct these mistakes, which is what Maquat studied in her work. In 1981, she discovered a molecular quality-control system that spots and destroys such incorrectly assembled mRNA. With the cryptic name "nonsense-mediated mRNA decay" or NMD, this process is vital to the health and wellbeing of a cellular kingdom in humans — because splicing mistakes happen far more often than one would imagine.
"We estimate that about a third of our mRNA are mistakes," Maquat says. "And nonsense-mediated mRNA decay cleans up these mistakes." When this quality-control system malfunctions, defective mRNA forge faulty proteins, which mess up the cellular machinery and cause disease, including various forms of cancer.
Scientists' newfound appreciation of RNA opens door to many novel treatments.
Now that the first RNA-based shots were approved, the same principle can be used for create vaccines for other diseases, the two RNA researchers say. Moreover, the molecule has an even greater potential — it can serve as a therapeutic target for other disorders. For example, Spinraza, a groundbreaking drug approved in 2016 for spinal muscular atrophy, uses small snippets of synthetic genetic material that bind to the RNA, helping fix splicing errors. "People can now appreciate why some of us studied RNA for such a long time," says Maquat.
Steitz is thrilled that the entire field of RNA research is enjoying the limelight. "I'm delighted because the prize is more of a recognition of the field than just our work," she says. "This is a more general acknowledgment of how basic research can have a remarkable impact on human health."
Lina Zeldovich has written about science, medicine and technology for Popular Science, Smithsonian, National Geographic, Scientific American, Reader’s Digest, the New York Times and other major national and international publications. A Columbia J-School alumna, she has won several awards for her stories, including the ASJA Crisis Coverage Award for Covid reporting, and has been a contributing editor at Nautilus Magazine. In 2021, Zeldovich released her first book, The Other Dark Matter, published by the University of Chicago Press, about the science and business of turning waste into wealth and health. You can find her on http://linazeldovich.com/ and @linazeldovich.
Indigenous wisdom plus honeypot ants could provide new antibiotics
For generations, the Indigenous Tjupan people of Australia enjoyed the sweet treat of honey made by honeypot ants. As a favorite pastime, entire families would go searching for the underground colonies, first spotting a worker ant and then tracing it to its home. The ants, which belong to the species called Camponotus inflatus, usually build their subterranean homes near the mulga trees, Acacia aneura. Having traced an ant to its tree, it would be the women who carefully dug a pit next to a colony, cautious not to destroy the entire structure. Once the ant chambers were exposed, the women would harvest a small amount to avoid devastating the colony’s stocks—and the family would share the treat.
The Tjupan people also knew that the honey had antimicrobial properties. “You could use it for a sore throat,” says Danny Ulrich, a member of the Tjupan nation. “You could also use it topically, on cuts and things like that.”
These hunts have become rarer, as many of the Tjupan people have moved away and, up until now, the exact antimicrobial properties of the ant honey remained unknown. But recently, scientists Andrew Dong and Kenya Fernandes from the University of Sydney, joined Ulrich, who runs the Honeypot Ants tours in Kalgoorlie, a city in Western Australia, on a honey-gathering expedition. Afterwards, they ran a series of experiments analyzing the honey’s antimicrobial activity—and confirmed that the Indigenous wisdom was true. The honey was effective against Staphylococcus aureus, a common pathogen responsible for sore throats, skin infections like boils and sores, and also sepsis, which can result in death. Moreover, the honey also worked against two species of fungi, Cryptococcus and Aspergillus, which can be pathogenic to humans, especially those with suppressed immune systems.
In the era of growing antibiotic resistance and the rising threat of pathogenic fungi, these findings may help scientists identify and make new antimicrobial compounds. “Natural products have been honed over thousands and millions of years by nature and evolution,” says Fernandes. “And some of them have complex and intricate properties that make them really important as potential new antibiotics. “
In an era of growing resistance to antibiotics and new threats of fungi infections, the latest findings about honeypot ants are helping scientists identify new antimicrobial drugs.
Danny Ulrich
Bee honey is also known for its antimicrobial properties, but bees produce it very differently than the ants. Bees collect nectar from flowers, which they regurgitate at the hive and pack into the hexagonal honeycombs they build for storage. As they do so, they also add into the mix an enzyme called glucose oxidase produced by their glands. The enzyme converts atmospheric oxygen into hydrogen peroxide, a reactive molecule that destroys bacteria and acts as a natural preservative. After the bees pack the honey into the honeycombs, they fan it with their wings to evaporate the water. Once a honeycomb is full, the bees put a beeswax cover on it, where it stays well-preserved thanks to the enzymatic action, until the bees need it.
Less is known about the chemistry of ants’ honey-making. Similarly to bees, they collect nectar. They also collect the sweet sap of the mulga tree. Additionally, they also “milk” the aphids—small sap-sucking insects that live on the tree. When ants tickle the aphids with their antennae, the latter release a sweet substance, which the former also transfer to their colonies. That’s where the honey management difference becomes really pronounced. The ants don’t build any kind of structures to store their honey. Instead, they store it in themselves.
The workers feed their harvest to their fellow ants called repletes, stuffing them up to the point that their swollen bellies outgrow the ants themselves, looking like amber-colored honeypots—hence the name. Because of their size, repletes don’t move, but hang down from the chamber’s ceiling, acting as living feedstocks. When food becomes scarce, they regurgitate their reserves to their colony’s brethren. It’s not clear whether the repletes die afterwards or can be restuffed again. “That's a good question,” Dong says. “After they've been stretched, they can't really return to exactly the same shape.”
These replete ants are the “treat” the Tjupan women dug for. Once they saw the round-belly ants inside the chambers, they would reach in carefully and get a few scoops of them. “You see a lot of honeypot ants just hanging on the roof of the little openings,” says Ulrich’s mother, Edie Ulrich. The women would share the ants with family members who would eat them one by one. “They're very delicate,” shares Edie Ulrich—you have to take them out carefully, so they don’t accidentally pop and become a wasted resource. “Because you’d lose all this precious honey.”
Dong stumbled upon the honeypot ants phenomenon because he was interested in Indigenous foods and went on Ulrich’s tour. He quickly became fascinated with the insects and their role in the Indigenous culture. “The honeypot ants are culturally revered by the Indigenous people,” he says. Eventually he decided to test out the honey’s medicinal qualities.
The researchers were surprised to see that even the smallest, eight percent concentration of honey was able to arrest the growth of S. aureus.
To do this, the two scientists first diluted the ant honey with water. “We used something called doubling dilutions, which means that we made 32 percent dilutions, and then we halve that to 16 percent and then we half that to eight percent,” explains Fernandes. The goal was to obtain as much results as possible with the meager honey they had. “We had very, very little of the honeypot ant honey so we wanted to maximize the spectrum of results we can get without wasting too much of the sample.”
After that, the researchers grew different microbes inside a nutrient rich broth. They added the broth to the different honey dilutions and incubated the mixes for a day or two at the temperature favorable to the germs’ growth. If the resulting solution turned turbid, it was a sign that the bugs proliferated. If it stayed clear, it meant that the honey destroyed them. The researchers were surprised to see that even the smallest, eight percent concentration of honey was able to arrest the growth of S. aureus. “It was really quite amazing,” Fernandes says. “Eight milliliters of honey in 92 milliliters of water is a really tiny amount of honey compared to the amount of water.”
Similar to bee honey, the ants’ honey exhibited some peroxide antimicrobial activity, researchers found, but given how little peroxide was in the solution, they think the honey also kills germs by a different mechanism. “When we measured, we found that [the solution] did have some hydrogen peroxide, but it didn't have as much of it as we would expect based on how active it was,” Fernandes says. “Whether this hydrogen peroxide also comes from glucose oxidase or whether it's produced by another source, we don't really know,” she adds. The research team does have some hypotheses about the identity of this other germ-killing agent. “We think it is most likely some kind of antimicrobial peptide that is actually coming from the ant itself.”
The honey also has a very strong activity against the two types of fungi, Cryptococcus and Aspergillus. Both fungi are associated with trees and decaying leaves, as well as in the soils where ants live, so the insects likely have evolved some natural defense compounds, which end up inside the honey.
It wouldn’t be the first time when modern medicines take their origin from the natural world or from the indigenous people’s knowledge. The bark of the cinchona tree native to South America contains quinine, a substance that treats malaria. The Indigenous people of the Andes used the bark to quell fever and chills for generations, and when Europeans began to fall ill with malaria in the Amazon rainforest, they learned to use that medicine from the Andean people.
The wonder drug aspirin similarly takes its origin from a bark of a tree—in this case a willow.
Even some anticancer compounds originated from nature. A chemotherapy drug called Paclitaxel, was originally extracted from the Pacific yew trees, Taxus brevifolia. The samples of the Pacific yew bark were first collected in 1962 by researchers from the United States Department of Agriculture who were looking for natural compounds that might have anti-tumor activity. In December 1992, the FDA approved Paclitaxel (brand name Taxol) for the treatment of ovarian cancer and two years later for breast cancer.
In the era when the world is struggling to find new medicines fast enough to subvert a fungal or bacterial pandemic, these discoveries can pave the way to new therapeutics. “I think it's really important to listen to indigenous cultures and to take their knowledge because they have been using these sources for a really, really long time,” Fernandes says. Now we know it works, so science can elucidate the molecular mechanisms behind it, she adds. “And maybe it can even provide a lead for us to develop some kind of new treatments in the future.”
Lina Zeldovich has written about science, medicine and technology for Popular Science, Smithsonian, National Geographic, Scientific American, Reader’s Digest, the New York Times and other major national and international publications. A Columbia J-School alumna, she has won several awards for her stories, including the ASJA Crisis Coverage Award for Covid reporting, and has been a contributing editor at Nautilus Magazine. In 2021, Zeldovich released her first book, The Other Dark Matter, published by the University of Chicago Press, about the science and business of turning waste into wealth and health. You can find her on http://linazeldovich.com/ and @linazeldovich.
Blood Test Can Detect Lymphoma Cells Before a Tumor Grows Back
When David M. Kurtz was doing his clinical fellowship at Stanford University Medical Center in 2009, specializing in lymphoma treatments, he found himself grappling with a question no one could answer. A typical regimen for these blood cancers prescribed six cycles of chemotherapy, but no one knew why. "The number seemed to be drawn out of a hat," Kurtz says. Some patients felt much better after just two doses, but had to endure the toxic effects of the entire course. For some elderly patients, the side effects of chemo are so harsh, they alone can kill. Others appeared to be cancer-free on the CT scans after the requisite six but then succumbed to it months later.
"Anecdotally, one patient decided to stop therapy after one dose because he felt it was so toxic that he opted for hospice instead," says Kurtz, now an oncologist at the center. "Five years down the road, he was alive and well. For him, just one dose was enough." Others would return for their one-year check up and find that their tumors grew back. Kurtz felt that while CT scans and MRIs were powerful tools, they weren't perfect ones. They couldn't tell him if there were any cancer cells left, stealthily waiting to germinate again. The scans only showed the tumor once it was back.
Blood cancers claim about 68,000 people a year, with a new diagnosis made about every three minutes, according to the Leukemia Research Foundation. For patients with B-cell lymphoma, which Kurtz focuses on, the survival chances are better than for some others. About 60 percent are cured, but the remaining 40 percent will relapse—possibly because they will have a negative CT scan, but still harbor malignant cells. "You can't see this on imaging," says Michael Green, who also treats blood cancers at University of Texas MD Anderson Medical Center.
The new blood test is sensitive enough to spot one cancerous perpetrator amongst one million other DNA molecules.
Kurtz wanted a better diagnostic tool, so he started working on a blood test that could capture the circulating tumor DNA or ctDNA. For that, he needed to identify the specific mutations typical for B-cell lymphomas. Working together with another fellow PhD student Jake Chabon, Kurtz finally zeroed-in on the tumor's genetic "appearance" in 2017—a pair of specific mutations sitting in close proximity to each other—a rare and telling sign. The human genome contains about 3 billion base pairs of nucleotides—molecules that compose genes—and in case of the B-cell lymphoma cells these two mutations were only a few base pairs apart. "That was the moment when the light bulb went on," Kurtz says.
The duo formed a company named Foresight Diagnostics, focusing on taking the blood test to the clinic. But knowing the tumor's mutational signature was only half the process. The other was fishing the tumor's DNA out of patients' bloodstream that contains millions of other DNA molecules, explains Chabon, now Foresight's CEO. It would be like looking for an escaped criminal in a large crowd. Kurtz and Chabon solved the problem by taking the tumor's "mug shot" first. Doctors would take the biopsy pre-treatment and sequence the tumor, as if taking the criminal's photo. After treatments, they would match the "mug shot" to all DNA molecules derived from the patient's blood sample to see if any molecular criminals managed to escape the chemo.
Foresight isn't the only company working on blood-based tumor detection tests, which are dubbed liquid biopsies—other companies such as Natera or ArcherDx developed their own. But in a recent study, the Foresight team showed that their method is significantly more sensitive in "fishing out" the cancer molecules than existing tests. Chabon says that this test can detect circulating tumor DNA in concentrations that are nearly 100 times lower than other methods. Put another way, it's sensitive enough to spot one cancerous perpetrator amongst one million other DNA molecules.
They also aim to extend their test to detect other malignancies such as lung, breast or colorectal cancers.
"It increases the sensitivity of detection and really catches most patients who are going to progress," says Green, the University of Texas oncologist who wasn't involved in the study, but is familiar with the method. It would also allow monitoring patients during treatment and making better-informed decisions about which therapy regimens would be most effective. "It's a minimally invasive test," Green says, and "it gives you a very high confidence about what's going on."
Having shown that the test works well, Kurtz and Chabon are planning a new trial in which oncologists would rely on their method to decide when to stop or continue chemo. They also aim to extend their test to detect other malignancies such as lung, breast or colorectal cancers. The latest genome sequencing technologies have sequenced and catalogued over 2,500 different tumor specimens and the Foresight team is analyzing this data, says Chabon, which gives the team the opportunity to create more molecular "mug shots."
The team hopes that that their blood cancer test will become available to patients within about five years, making doctors' job easier, and not only at the biological level. "When I tell patients, "good news, your cancer is in remission', they ask me, 'does it mean I'm cured?'" Kurtz says. "Right now I can't answer this question because I don't know—but I would like to." His company's test, he hopes, will enable him to reply with certainty. He'd very much like to have the power of that foresight.
This article is republished from our archives to coincide with Blood Cancer Awareness Month, which highlights progress in cancer diagnostics and treatment.
Lina Zeldovich has written about science, medicine and technology for Popular Science, Smithsonian, National Geographic, Scientific American, Reader’s Digest, the New York Times and other major national and international publications. A Columbia J-School alumna, she has won several awards for her stories, including the ASJA Crisis Coverage Award for Covid reporting, and has been a contributing editor at Nautilus Magazine. In 2021, Zeldovich released her first book, The Other Dark Matter, published by the University of Chicago Press, about the science and business of turning waste into wealth and health. You can find her on http://linazeldovich.com/ and @linazeldovich.