Inside Scoop: How a DARPA Scientist Helped Usher in a Game-Changing Covid Treatment
Amy Jenkins was in her office at DARPA, a research and development agency within the Department of Defense, when she first heard about a respiratory illness plaguing the Chinese city of Wuhan. Because she's a program manager for DARPA's Biological Technologies Office, her colleagues started stopping by. "It's really unusual, isn't it?" they would say.
At the time, China had a few dozen cases of what we now call COVID-19. "We should maybe keep an eye on that," she thought.
Early in 2020, still just keeping watch, she was visiting researchers working on DARPA's Pandemic Prevention Platform (P3), a project to develop treatments for "any known or previously unknown infectious threat," within 60 days of its appearance. "We looked at each other and said, 'Should we be doing something?'" she says.
For projects like P3, groups of scientists—often at universities and private companies—compete for DARPA contracts, and program managers like Jenkins oversee the work. Those that won the P3 bid included scientists at AbCellera Biologics, Inc., AstraZeneca, Duke University, and Vanderbilt University.
At the time Jenkins was talking to the P3 performers, though, they didn't have evidence of community transmission. "We would have to cross that bar before we considered doing anything," she says.
The world soon leapt far over that bar. By the time Jenkins and her team decided P3 should be doing something—with their real work beginning in late February--it was too late to prevent this pandemic. But she could help P3 dig into the chemical foundations of COVID-19's malfeasance, and cut off its roots. That work represents, in fact, her roots.
In late February 2020, DARPA received a single blood sample from a recovered COVID-19 patient, in which P3 researchers could go fishing for antibodies. The day it arrived, Jenkins's stomach roiled. "We get one shot," she thought.
Fighting the Smallest Enemies
Jenkins, who's in her early 40s, first got into germs the way many 90s kids did: by reading The Hot Zone, a novel about a hemorrhagic fever gone rogue. It wasn't exactly the disintegrating organs that hooked her. It was the idea that "these very pathogens that we can't even see can make us so sick and bring us to our knees," she says. Reading about scientists facing down deadly disease, she wondered, "How do these things make you so sick?"
She chased that question in college, majoring in both biomolecular science and chemistry, and later became an antibody expert. Antibodies are proteins that hook to a pathogen to block it from attaching to your cells, or tag it for destruction by the rest of the immune system. Soon, she jumped on the "monoclonal antibodies" train—developing synthetic versions of these natural defenses, which doctors can give to people to help them battle an early-stage infection, and even to prevent an infection from taking root after an exposure.
Jenkins likens the antibody treatments to the old aphorism about fishing: Vaccines teach your body how to fish, but antibodies simply give your body the pesca-fare. While that, as the saying goes, won't feed you for a lifetime, it will last a few weeks or months. Monoclonal antibodies thus are a promising preventative option in the immediate short-term when a vaccine hasn't yet been given (or hasn't had time to produce an immune response), as well as an important treatment weapon in the current fight. After former president Donald Trump contracted COVID-19, he received a monoclonal antibody treatment from biotech company Regeneron.
As for Jenkins, she started working as a DARPA Biological Technologies Office contractor soon after completing her postdoc. But it was a suit job, not a labcoat job. And suit jobs, at first, left Jenkins conflicted, worried about being bored. She'd give it a year, she thought. But the year expired, and bored she was not. Around five years later, in June 2019, the agency hired her to manage several of the office's programs. A year into that gig, the world was months into a pandemic.
The Pandemic Pivot
At DARPA, Jenkins inherited five programs, including P3. P3 works by taking blood from recovered people, fishing out their antibodies, identifying the most effective ones, and then figuring out how to manufacture them fast. Back then, P3 existed to help with nebulous, future outbreaks: Pandemic X. Not this pandemic. "I did not have a crystal ball," she says, "but I will say that all of us in the infectious diseases and public-health realm knew that the next pandemic was coming."
Three days after a January 2020 meeting with P3 researchers, COVID-19 appeared in Seattle, then began whipping through communities. The time had come for P3 teams to swivel. "We had done this," she says. "We had practiced this before." But would their methods stand up to something unknown, racing through the global population? "The big anxiety was, 'Wow, this was real,'" says Jenkins.
While facing down that realness, Jenkins was also managing other projects. In one called PREPARE, groups develop "medical countermeasures" that modulate a person's genetic code to boost their bodies' responses to threats. Another project, NOW, envisions shipping-container-sized factories that can make thousands of vaccine doses in days. And then there's Prometheus—which means "forethought" in Greek, and is the name of the god who stole fire and gave it to humans. Wrapping up as COVID ramped up, Prometheus aimed to identify people who are contagious—with whatever—before they start coughing, and even if they never do.
All of DARPA's projects focus on developing early-stage technology, passing it off to other agencies or industry to put it into operation. The orientation toward a specific goal appealed to Jenkins, as a contrast to academia. "You go down a rabbit hole for years at a time sometimes, chasing some concept you found interesting in the lab," she says. That's good for the human pursuit of knowledge, and leads to later applications, but DARPA wants a practical prototype—stat.
That desire, though, and the fact that DARPA is a defense agency, present philosophical complications. "Bioethics in the national-security context turns all the dials up to 10+," says Jonathan Moreno, a medical ethicist at the University of Pennsylvania.
While developing antibody treatments to stem a pandemic seems straightforwardly good, all biological research—especially that backed by military money—requires evaluating potential knock-on applications, even those that might come from outside the entity that did the developing. As Moreno put it, "Albert Einstein wasn't thinking about blowing up Hiroshima." Particularly sensitive are so-called "dual-use" technologies—those tools that could be used for both benign and nefarious purposes, or are of interest to both the civilian and military worlds.
Moreno takes Prometheus itself as an example of "dual-use" technology. "Think about somebody wearing a suicide vest. Instead of a suicide vest, make them extremely contagious with something. The flu plus Ebola," he says. "Send them someplace, a sensitive environment. We would like to be able to defend against that"—not just tell whether Uncle Fred is bringing asymptomatic COVID home for Christmas. Prometheus, Jenkins says, had safety in mind from the get-go, and required contenders to "develop a risk mitigation plan" and "detail their strategy for appropriate control of information."
To look at a different program, if you can modulate genes to help healing, you probably know something (or know someone else could infer something) about how to hinder healing. Those sorts of risks are why PREPARE researchers got their own "ethical, legal, and social implications" panel, which meets quarterly "to ensure that we are performing all research and publications in a safe and ethical manner," says Jenkins.
DARPA as a whole, Moreno says, is institutionally sensitive to bioethics. The agency has ethics panels, and funded a 2014 National Academies assessment of how to address the "ethical, legal, and societal issues" around technology that has military relevance. "In the cases of biotechnologies where some of that research brushes up against what could legitimately be considered dual-use, that in itself justifies our investment," says Jenkins. "DARPA deliberately focuses on safety and countermeasures against potentially dangerous technologies, and we structure our programs to be transparent, safe, and legal."
In late February 2020, DARPA received a single blood sample from a recovered COVID-19 patient, in which P3 researchers could go fishing for antibodies. The day it arrived, Jenkins's stomach roiled. "We get one shot," she thought.
As scientists from the P3-funded AbCellera went through the processes they'd practiced, Jenkins managed their work, tracking progress and relaying results. Soon, the team had isolated a suitable protein: bamlanivimab. It attaches to and blocks off the infamous spike proteins on SARS-CoV-2—those sticky suction-cups in illustrations. Partnering with Eli Lilly in a manufacturing agreement, the biotech company brought it to clinical trials in May, just a few months after its work on the deadly pathogen began, after much of the planet became a hot zone.
On November 10—Jenkins's favorite day at the (home) office—the FDA provided Eli Lilly emergency use authorization for bamlanivimab. But she's only mutedly screaming (with joy) inside her heart. "This pandemic isn't 'one morning we're going to wake up and it's all over,'" she says. When it is over, she and her colleagues plan to celebrate their promethean work. "I'm hoping to be able to do it in person," she says. "Until then, I have not taken a breath."
Tiny, tough “water bears” may help bring new vaccines and medicines to sub-Saharan Africa
Microscopic tardigrades, widely considered to be some of the toughest animals on earth, can survive for decades without oxygen or water and are thought to have lived through a crash-landing on the moon. Also known as water bears, they survive by fully dehydrating and later rehydrating themselves – a feat only a few animals can accomplish. Now scientists are harnessing tardigrades’ talents to make medicines that can be dried and stored at ambient temperatures and later rehydrated for use—instead of being kept refrigerated or frozen.
Many biologics—pharmaceutical products made by using living cells or synthesized from biological sources—require refrigeration, which isn’t always available in many remote locales or places with unreliable electricity. These products include mRNA and other vaccines, monoclonal antibodies and immuno-therapies for cancer, rheumatoid arthritis and other conditions. Cooling is also needed for medicines for blood clotting disorders like hemophilia and for trauma patients.
Formulating biologics to withstand drying and hot temperatures has been the holy grail for pharmaceutical researchers for decades. It’s a hard feat to manage. “Biologic pharmaceuticals are highly efficacious, but many are inherently unstable,” says Thomas Boothby, assistant professor of molecular biology at University of Wyoming. Therefore, during storage and shipping, they must be refrigerated at 2 to 8 degrees Celsius (35 to 46 degrees Fahrenheit). Some must be frozen, typically at -20 degrees Celsius, but sometimes as low -90 degrees Celsius as was the case with the Pfizer Covid vaccine.
For Covid, fewer than 73 percent of the global population received even one dose. The need for refrigerated or frozen handling was partially to blame.
The costly cold chain
The logistics network that ensures those temperature requirements are met from production to administration is called the cold chain. This cold chain network is often unreliable or entirely lacking in remote, rural areas in developing nations that have malfunctioning electrical grids. “Almost all routine vaccines require a cold chain,” says Christopher Fox, senior vice president of formulations at the Access to Advanced Health Institute. But when the power goes out, so does refrigeration, putting refrigerated or frozen medical products at risk. Consequently, the mRNA vaccines developed for Covid-19 and other conditions, as well as more traditional vaccines for cholera, tetanus and other diseases, often can’t be delivered to the most remote parts of the world.
To understand the scope of the challenge, consider this: In the U.S., more than 984 million doses of Covid-19 vaccine have been distributed so far. Each one needed refrigeration that, even in the U.S., proved challenging. Now extrapolate to all vaccines and the entire world. For Covid, fewer than 73 percent of the global population received even one dose. The need for refrigerated or frozen handling was partially to blame.
Globally, the cold chain packaging market is valued at over $15 billion and is expected to exceed $60 billion by 2033.
Freeze-drying, also called lyophilization, which is common for many vaccines, isn’t always an option. Many freeze-dried vaccines still need refrigeration, and even medicines approved for storage at ambient temperatures break down in the heat of sub-Saharan Africa. “Even in a freeze-dried state, biologics often will undergo partial rehydration and dehydration, which can be extremely damaging,” Boothby explains.
The cold chain is also very expensive to maintain. The global pharmaceutical cold chain packaging market is valued at more than $15 billion, and is expected to exceed $60 billion by 2033, according to a report by Future Market Insights. This cost is only expected to grow. According to the consulting company Accenture, the number of medicines that require the cold chain are expected to grow by 48 percent, compared to only 21 percent for non-cold-chain therapies.
Tardigrades to the rescue
Tardigrades are only about a millimeter long – with four legs and claws, and they lumber around like bears, thus their nickname – but could provide a big solution. “Tardigrades are unique in the animal kingdom, in that they’re able to survive a vast array of environmental insults,” says Boothby, the Wyoming professor. “They can be dried out, frozen, heated past the boiling point of water and irradiated at levels that are thousands of times more than you or I could survive.” So, his team is gradually unlocking tardigrades’ survival secrets and applying them to biologic pharmaceuticals to make them withstand both extreme heat and desiccation without losing efficacy.
Boothby’s team is focusing on blood clotting factor VIII, which, as the name implies, causes blood to clot. Currently, Boothby is concentrating on the so-called cytoplasmic abundant heat soluble (CAHS) protein family, which is found only in tardigrades, protecting them when they dry out. “We showed we can desiccate a biologic (blood clotting factor VIII, a key clotting component) in the presence of tardigrade proteins,” he says—without losing any of its effectiveness.
The researchers mixed the tardigrade protein with the blood clotting factor and then dried and rehydrated that substance six times without damaging the latter. This suggests that biologics protected with tardigrade proteins can withstand real-world fluctuations in humidity.
Furthermore, Boothby’s team found that when the blood clotting factor was dried and stabilized with tardigrade proteins, it retained its efficacy at temperatures as high as 95 degrees Celsius. That’s over 200 degrees Fahrenheit, much hotter than the 58 degrees Celsius that the World Meteorological Organization lists as the hottest recorded air temperature on earth. In contrast, without the protein, the blood clotting factor degraded significantly. The team published their findings in the journal Nature in March.
Although tardigrades rarely live more than 2.5 years, they have survived in a desiccated state for up to two decades, according to Animal Diversity Web. This suggests that tardigrades’ CAHS protein can protect biologic pharmaceuticals nearly indefinitely without refrigeration or freezing, which makes it significantly easier to deliver them in locations where refrigeration is unreliable or doesn’t exist.
The tricks of the tardigrades
Besides the CAHS proteins, tardigrades rely on a type of sugar called trehalose and some other protectants. So, rather than drying up, their cells solidify into rigid, glass-like structures. As that happens, viscosity between cells increases, thereby slowing their biological functions so much that they all but stop.
Now Boothby is combining CAHS D, one of the proteins in the CAHS family, with trehalose. He found that CAHS D and trehalose each protected proteins through repeated drying and rehydrating cycles. They also work synergistically, which means that together they might stabilize biologics under a variety of dry storage conditions.
“We’re finding the protective effect is not just additive but actually is synergistic,” he says. “We’re keen to see if something like that also holds true with different protein combinations.” If so, combinations could possibly protect against a variety of conditions.
Before any stabilization technology for biologics can be commercialized, it first must be approved by the appropriate regulators. In the U.S., that’s the U.S. Food and Drug Administration. Developing a new formulation would require clinical testing and vast numbers of participants. So existing vaccines and biologics likely won’t be re-formulated for dry storage. “Many were developed decades ago,” says Fox. “They‘re not going to be reformulated into thermo-stable vaccines overnight,” if ever, he predicts.
Extending stability outside the cold chain, even for a few days, can have profound health, environmental and economic benefits.
Instead, this technology is most likely to be used for the new products and formulations that are just being created. New and improved vaccines will be the first to benefit. Good candidates include the plethora of mRNA vaccines, as well as biologic pharmaceuticals for neglected diseases that affect parts of the world where reliable cold chain is difficult to maintain, Boothby says. Some examples include new, more effective vaccines for malaria and for pathogenic Escherichia coli, which causes diarrhea.
Tallying up the benefits
Extending stability outside the cold chain, even for a few days, can have profound health, environmental and economic benefits. For instance, MenAfriVac, a meningitis vaccine (without tardigrade proteins) developed for sub-Saharan Africa, can be stored at up to 40 degrees Celsius for four days before administration. “If you have a few days where you don’t need to maintain the cold chain, it’s easier to transport vaccines to remote areas,” Fox says, where refrigeration does not exist or is not reliable.
Better health is an obvious benefit. MenAfriVac reduced suspected meningitis cases by 57 percent in the overall population and more than 99 percent among vaccinated individuals.
Lower healthcare costs are another benefit. One study done in Togo found that the cold chain-related costs increased the per dose vaccine price up to 11-fold. The ability to ship the vaccines using the usual cold chain, but transporting them at ambient temperatures for the final few days cut the cost in half.
There are environmental benefits, too, such as reducing fuel consumption and greenhouse gas emissions. Cold chain transports consume 20 percent more fuel than non-cold chain shipping, due to refrigeration equipment, according to the International Trade Administration.
A study by researchers at Johns Hopkins University compared the greenhouse gas emissions of the new, oral Vaxart COVID-19 vaccine (which doesn’t require refrigeration) with four intramuscular vaccines (which require refrigeration or freezing). While the Vaxart vaccine is still in clinical trials, the study found that “up to 82.25 million kilograms of CO2 could be averted by using oral vaccines in the U.S. alone.” That is akin to taking 17,700 vehicles out of service for one year.
Although tardigrades’ protective proteins won’t be a component of biologic pharmaceutics for several years, scientists are proving that this approach is viable. They are hopeful that a day will come when vaccines and biologics can be delivered anywhere in the world without needing refrigerators or freezers en route.
Man Who Got the First Fecal Transplant to Cure Melanoma Shares His Experience
Jamie Rettinger was still in his thirties when he first noticed a tiny streak of brown running through the thumbnail of his right hand. It slowly grew wider and the skin underneath began to deteriorate before he went to a local dermatologist in 2013. The doctor thought it was a wart and tried scooping it out, treating the affected area for three years before finally removing the nail bed and sending it off to a pathology lab for analysis.
"I have some bad news for you; what we removed was a five-millimeter melanoma, a cancerous tumor that often spreads," Jamie recalls being told on his return visit. "I'd never heard of cancer coming through a thumbnail," he says. None of his doctors had ever mentioned it either. "I just thought I was being treated for a wart." But nothing was healing and it continued to bleed.
A few months later a surgeon amputated the top half of his thumb. Lymph node biopsy tested negative for spread of the cancer and when the bandages finally came off, Jamie thought his medical issues were resolved.
Melanoma is the deadliest form of skin cancer. About 85,000 people are diagnosed with it each year in the U.S. and more than 8,000 die of the cancer when it spreads to other parts of the body, according to the Centers for Disease Control and Prevention (CDC).
There are two peaks in diagnosis of melanoma; one is in younger women ages 30-40 and often is tied to past use of tanning beds; the second is older men 60+ and is related to outdoor activity from farming to sports. Light-skinned people have a twenty-times greater risk of melanoma than do people with dark skin.
"When I graduated from medical school, in 2005, melanoma was a death sentence" --Diwakar Davar.
Jamie had a follow up PET scan about six months after his surgery. A suspicious spot on his lung led to a biopsy that came back positive for melanoma. The cancer had spread. Treatment with a monoclonal antibody (nivolumab/Opdivo®) didn't prove effective and he was referred to the UPMC Hillman Cancer Center in Pittsburgh, a four-hour drive from his home in western Ohio.
An alternative monoclonal antibody treatment brought on such bad side effects, diarrhea as often as 15 times a day, that it took more than a week of hospitalization to stabilize his condition. The only options left were experimental approaches in clinical trials.
"When I graduated from medical school, in 2005, melanoma was a death sentence" with a cure rate in the single digits, says Diwakar Davar, 39, an oncologist at UPMC Hillman Cancer Center who specializes in skin cancer. That began to change in 2010 with introduction of the first immunotherapies, monoclonal antibodies, to treat cancer. The antibodies attach to PD-1, a receptor on the surface of T cells of the immune system and on cancer cells. Antibody treatment boosted the melanoma cure rate to about 30 percent. The search was on to understand why some people responded to these drugs and others did not.
At the same time, there was a growing understanding of the role that bacteria in the gut, the gut microbiome, plays in helping to train and maintain the function of the body's various immune cells. Perhaps the bacteria also plays a role in shaping the immune response to cancer therapy.
One clue came from genetically identical mice. Animals ordered from different suppliers sometimes responded differently to the experiments being performed. That difference was traced to different compositions of their gut microbiome; transferring the microbiome from one animal to another in a process known as fecal transplant (FMT) could change their responses to disease or treatment.
When researchers looked at humans, they found that the patients who responded well to immunotherapies had a gut microbiome that looked like healthy normal folks, but patients who didn't respond had missing or reduced strains of bacteria.
Davar and his team knew that FMT had a very successful cure rate in treating the gut dysbiosis of Clostridioides difficile, a persistant intestinal infection, and they wondered if a fecal transplant from a patient who had responded well to cancer immunotherapy treatment might improve the cure rate of patients who did not originally respond to immunotherapies for melanoma.
The ABCDE of melanoma detection
"It was pretty weird, I was totally blasted away. Who had thought of this?" Jamie first thought when the hypothesis was explained to him. But Davar's explanation that the procedure might restore some of the beneficial bacterial his gut was lacking, convinced him to try. He quickly signed on in October 2018 to be the first person in the clinical trial.
Fecal donations go through the same safety procedures of screening for and inactivating diseases that are used in processing blood donations to make them safe for transfusion. The procedure itself uses a standard hollow colonoscope designed to screen for colon cancer and remove polyps. The transplant is inserted through the center of the flexible tube.
Most patients are sedated for procedures that use a colonoscope but Jamie doesn't respond to those drugs: "You can't knock me out. I was watching them on the TV going up my own butt. It was kind of unreal at that point," he says. "There were about twelve people in there watching because no one had seen this done before."
A test two weeks after the procedure showed that the FMT had engrafted and the once-missing bacteria were thriving in his gut. More importantly, his body was responding to another monoclonal antibody (pembrolizumab/Keytruda®) and signs of melanoma began to shrink. Every three months he made the four-hour drive from home to Pittsburgh for six rounds of treatment with the antibody drug.
"We were very, very lucky that the first patient had a great response," says Davar. "It allowed us to believe that even though we failed with the next six, we were on the right track. We just needed to tweak the [fecal] cocktail a little better" and enroll patients in the study who had less aggressive tumor growth and were likely to live long enough to complete the extensive rounds of therapy. Six of 15 patients responded positively in the pilot clinical trial that was published in the journal Science.
Davar believes they are beginning to understand the biological mechanisms of why some patients initially do not respond to immunotherapy but later can with a FMT. It is tied to the background level of inflammation produced by the interaction between the microbiome and the immune system. That paper is not yet published.
It has been almost a year since the last in his series of cancer treatments and Jamie has no measurable disease. He is cautiously optimistic that his cancer is not simply in remission but is gone for good. "I'm still scared every time I get my scans, because you don't know whether it is going to come back or not. And to realize that it is something that is totally out of my control."
"It was hard for me to regain trust" after being misdiagnosed and mistreated by several doctors he says. But his experience at Hillman helped to restore that trust "because they were interested in me, not just fixing the problem."
He is grateful for the support provided by family and friends over the last eight years. After a pause and a sigh, the ruggedly built 47-year-old says, "If everyone else was dead in my family, I probably wouldn't have been able to do it."
"I never hesitated to ask a question and I never hesitated to get a second opinion." But Jamie acknowledges the experience has made him more aware of the need for regular preventive medical care and a primary care physician. That person might have caught his melanoma at an earlier stage when it was easier to treat.
Davar continues to work on clinical studies to optimize this treatment approach. Perhaps down the road, screening the microbiome will be standard for melanoma and other cancers prior to using immunotherapies, and the FMT will be as simple as swallowing a handful of freeze-dried capsules off the shelf rather than through a colonoscopy. Earlier this year, the Food and Drug Administration approved the first oral fecal microbiota product for C. difficile, hopefully paving the way for more.
An older version of this hit article was first published on May 18, 2021