Regenerative medicine has come a long way, baby
The field of regenerative medicine had a shaky start. In 2002, when news spread about the first cloned animal, Dolly the sheep, a raucous debate ensued. Scary headlines and organized opposition groups put pressure on government leaders, who responded by tightening restrictions on this type of research.
Fast forward to today, and regenerative medicine, which focuses on making unhealthy tissues and organs healthy again, is rewriting the code to healing many disorders, though it’s still young enough to be considered nascent. What started as one of the most controversial areas in medicine is now promising to transform it.
Progress in the lab has addressed previous concerns. Back in the early 2000s, some of the most fervent controversy centered around somatic cell nuclear transfer (SCNT), the process used by scientists to produce Dolly. There was fear that this technique could be used in humans, with possibly adverse effects, considering the many medical problems of the animals who had been cloned.
But today, scientists have discovered better approaches with fewer risks. Pioneers in the field are embracing new possibilities for cellular reprogramming, 3D organ printing, AI collaboration, and even growing organs in space. It could bring a new era of personalized medicine for longer, healthier lives - while potentially sparking new controversies.
Engineering tissues from amniotic fluids
Work in regenerative medicine seeks to reverse damage to organs and tissues by culling, modifying and replacing cells in the human body. Scientists in this field reach deep into the mechanisms of diseases and the breakdowns of cells, the little workhorses that perform all life-giving processes. If cells can’t do their jobs, they take whole organs and systems down with them. Regenerative medicine seeks to harness the power of healthy cells derived from stem cells to do the work that can literally restore patients to a state of health—by giving them healthy, functioning tissues and organs.
Modern-day regenerative medicine takes its origin from the 1998 isolation of human embryonic stem cells, first achieved by John Gearhart at Johns Hopkins University. Gearhart isolated the pluripotent cells that can differentiate into virtually every kind of cell in the human body. There was a raging controversy about the use of these cells in research because at that time they came exclusively from early-stage embryos or fetal tissue.
Back then, the highly controversial SCNT cells were the only way to produce genetically matched stem cells to treat patients. Since then, the picture has changed radically because other sources of highly versatile stem cells have been developed. Today, scientists can derive stem cells from amniotic fluid or reprogram patients’ skin cells back to an immature state, so they can differentiate into whatever types of cells the patient needs.
In the context of medical history, the field of regenerative medicine is progressing at a dizzying speed. But for those living with aggressive or chronic illnesses, it can seem that the wheels of medical progress grind slowly.
The ethical debate has been dialed back and, in the last few decades, the field has produced important innovations, spurring the development of whole new FDA processes and categories, says Anthony Atala, a bioengineer and director of the Wake Forest Institute for Regenerative Medicine. Atala and a large team of researchers have pioneered many of the first applications of 3D printed tissues and organs using cells developed from patients or those obtained from amniotic fluid or placentas.
His lab, considered to be the largest devoted to translational regenerative medicine, is currently working with 40 different engineered human tissues. Sixteen of them have been transplanted into patients. That includes skin, bladders, urethras, muscles, kidneys and vaginal organs, to name just a few.
These achievements are made possible by converging disciplines and technologies, such as cell therapies, bioengineering, gene editing, nanotechnology and 3D printing, to create living tissues and organs for human transplants. Atala is currently overseeing clinical trials to test the safety of tissues and organs engineered in the Wake Forest lab, a significant step toward FDA approval.
In the context of medical history, the field of regenerative medicine is progressing at a dizzying speed. But for those living with aggressive or chronic illnesses, it can seem that the wheels of medical progress grind slowly.
“It’s never fast enough,” Atala says. “We want to get new treatments into the clinic faster, but the reality is that you have to dot all your i’s and cross all your t’s—and rightly so, for the sake of patient safety. People want predictions, but you can never predict how much work it will take to go from conceptualization to utilization.”
As a surgeon, he also treats patients and is able to follow transplant recipients. “At the end of the day, the goal is to get these technologies into patients, and working with the patients is a very rewarding experience,” he says. Will the 3D printed organs ever outrun the shortage of donated organs? “That’s the hope,” Atala says, “but this technology won’t eliminate the need for them in our lifetime.”
New methods are out of this world
Jeanne Loring, another pioneer in the field and director of the Center for Regenerative Medicine at Scripps Research Institute in San Diego, says that investment in regenerative medicine is not only paying off, but is leading to truly personalized medicine, one of the holy grails of modern science.
This is because a patient’s own skin cells can be reprogrammed to become replacements for various malfunctioning cells causing incurable diseases, such as diabetes, heart disease, macular degeneration and Parkinson’s. If the cells are obtained from a source other than the patient, they can be rejected by the immune system. This means that patients need lifelong immunosuppression, which isn’t ideal. “With Covid,” says Loring, “I became acutely aware of the dangers of immunosuppression.” Using the patient’s own cells eliminates that problem.
Microgravity conditions make it easier for the cells to form three-dimensional structures, which could more easily lead to the growing of whole organs. In fact, Loring's own cells have been sent to the ISS for study.
Loring has a special interest in neurons, or brain cells that can be developed by manipulating cells found in the skin. She is looking to eventually treat Parkinson’s disease using them. The manipulated cells produce dopamine, the critical hormone or neurotransmitter lacking in the brains of patients. A company she founded plans to start a Phase I clinical trial using cell therapies for Parkinson’s soon, she says.
This is the culmination of many years of basic research on her part, some of it on her own cells. In 2007, Loring had her own cells reprogrammed, so there’s a cell line that carries her DNA. “They’re just like embryonic stem cells, but personal,” she said.
Loring has another special interest—sending immature cells into space to be studied at the International Space Station. There, microgravity conditions make it easier for the cells to form three-dimensional structures, which could more easily lead to the growing of whole organs. In fact, her own cells have been sent to the ISS for study. “My colleagues and I have completed four missions at the space station,” she says. “The last cells came down last August. They were my own cells reprogrammed into pluripotent cells in 2009. No one else can say that,” she adds.
Future controversies and tipping points
Although the original SCNT debate has calmed down, more controversies may arise, Loring thinks.
One of them could concern growing synthetic embryos. The embryos are ultimately derived from embryonic stem cells, and it’s not clear to what stage these embryos can or will be grown in an artificial uterus—another recent invention. The science, so far done only in animals, is still new and has not been widely publicized but, eventually, “People will notice the production of synthetic embryos and growing them in an artificial uterus,” Loring says. It’s likely to incite many of the same reactions as the use of embryonic stem cells.
Bernard Siegel, the founder and director of the Regenerative Medicine Foundation and executive director of the newly formed Healthspan Action Coalition (HSAC), believes that stem cell science is rapidly approaching tipping point and changing all of medical science. (For disclosure, I do consulting work for HSAC). Siegel says that regenerative medicine has become a new pillar of medicine that has recently been fast-tracked by new technology.
Artificial intelligence is speeding up discoveries and the convergence of key disciplines, as demonstrated in Atala’s lab, which is creating complex new medical products that replace the body’s natural parts. Just as importantly, those parts are genetically matched and pose no risk of rejection.
These new technologies must be regulated, which can be a challenge, Siegel notes. “Cell therapies represent a challenge to the existing regulatory structure, including payment, reimbursement and infrastructure issues that 20 years ago, didn’t exist.” Now the FDA and other agencies are faced with this revolution, and they’re just beginning to adapt.
Siegel cited the 2021 FDA Modernization Act as a major step. The Act allows drug developers to use alternatives to animal testing in investigating the safety and efficacy of new compounds, loosening the agency’s requirement for extensive animal testing before a new drug can move into clinical trials. The Act is a recognition of the profound effect that cultured human cells are having on research. Being able to test drugs using actual human cells promises to be far safer and more accurate in predicting how they will act in the human body, and could accelerate drug development.
Siegel, a longtime veteran and founding father of several health advocacy organizations, believes this work helped bring cell therapies to people sooner rather than later. His new focus, through the HSAC, is to leverage regenerative medicine into extending not just the lifespan but the worldwide human healthspan, the period of life lived with health and vigor. “When you look at the HSAC as a tree,” asks Siegel, “what are the roots of that tree? Stem cell science and the huge ecosystem it has created.” The study of human aging is another root to the tree that has potential to lengthen healthspans.
The revolutionary science underlying the extension of the healthspan needs to be available to the whole world, Siegel says. “We need to take all these roots and come up with a way to improve the life of all mankind,” he says. “Everyone should be able to take advantage of this promising new world.”
Meet the Scientists on the Frontlines of Protecting Humanity from a Man-Made Pathogen
Jean Peccoud wasn't expecting an email from the FBI. He definitely wasn't expecting the agency to invite him to a meeting. "My reaction was, 'What did I do wrong to be on the FBI watch list?'" he recalls.
You use those blueprints for white-hat research—which is, indeed, why the open blueprints exist—or you can do the same for a black-hat attack.
He didn't know what the feds could possibly want from him. "I was mostly scared at this point," he says. "I was deeply disturbed by the whole thing."
But he decided to go anyway, and when he traveled to San Francisco for the 2008 gathering, the reason for the e-vite became clear: The FBI was reaching out to researchers like him—scientists interested in synthetic biology—in anticipation of the potential nefarious uses of this technology. "The whole purpose of the meeting was, 'Let's start talking to each other before we actually need to talk to each other,'" says Peccoud, now a professor of chemical and biological engineering at Colorado State University. "'And let's make sure next time you get an email from the FBI, you don't freak out."
Synthetic biology—which Peccoud defines as "the application of engineering methods to biological systems"—holds great power, and with that (as always) comes great responsibility. When you can synthesize genetic material in a lab, you can create new ways of diagnosing and treating people, and even new food ingredients. But you can also "print" the genetic sequence of a virus or virulent bacterium.
And while it's not easy, it's also not as hard as it could be, in part because dangerous sequences have publicly available blueprints. You use those blueprints for white-hat research—which is, indeed, why the open blueprints exist—or you can do the same for a black-hat attack. You could synthesize a dangerous pathogen's code on purpose, or you could unwittingly do so because someone tampered with your digital instructions. Ordering synthetic genes for viral sequences, says Peccoud, would likely be more difficult today than it was a decade ago.
"There is more awareness of the industry, and they are taking this more seriously," he says. "There is no specific regulation, though."
Trying to lock down the interconnected machines that enable synthetic biology, secure its lab processes, and keep dangerous pathogens out of the hands of bad actors is part of a relatively new field: cyberbiosecurity, whose name Peccoud and colleagues introduced in a 2018 paper.
Biological threats feel especially acute right now, during the ongoing pandemic. COVID-19 is a natural pathogen -- not one engineered in a lab. But future outbreaks could start from a bug nature didn't build, if the wrong people get ahold of the right genetic sequences, and put them in the right sequence. Securing the equipment and processes that make synthetic biology possible -- so that doesn't happen -- is part of why the field of cyberbiosecurity was born.
The Origin Story
It is perhaps no coincidence that the FBI pinged Peccoud when it did: soon after a journalist ordered a sequence of smallpox DNA and wrote, for The Guardian, about how easy it was. "That was not good press for anybody," says Peccoud. Previously, in 2002, the Pentagon had funded SUNY Stonybrook researchers to try something similar: They ordered bits of polio DNA piecemeal and, over the course of three years, strung them together.
Although many years have passed since those early gotchas, the current patchwork of regulations still wouldn't necessarily prevent someone from pulling similar tricks now, and the technological systems that synthetic biology runs on are more intertwined — and so perhaps more hackable — than ever. Researchers like Peccoud are working to bring awareness to those potential problems, to promote accountability, and to provide early-detection tools that would catch the whiff of a rotten act before it became one.
Peccoud notes that if someone wants to get access to a specific pathogen, it is probably easier to collect it from the environment or take it from a biodefense lab than to whip it up synthetically. "However, people could use genetic databases to design a system that combines different genes in a way that would make them dangerous together without each of the components being dangerous on its own," he says. "This would be much more difficult to detect."
After his meeting with the FBI, Peccoud grew more interested in these sorts of security questions. So he was paying attention when, in 2010, the Department of Health and Human Services — now helping manage the response to COVID-19 — created guidance for how to screen synthetic biology orders, to make sure suppliers didn't accidentally send bad actors the sequences that make up bad genomes.
Guidance is nice, Peccoud thought, but it's just words. He wanted to turn those words into action: into a computer program. "I didn't know if it was something you can run on a desktop or if you need a supercomputer to run it," he says. So, one summer, he tasked a team of student researchers with poring over the sentences and turning them into scripts. "I let the FBI know," he says, having both learned his lesson and wanting to get in on the game.
Peccoud later joined forces with Randall Murch, a former FBI agent and current Virginia Tech professor, and a team of colleagues from both Virginia Tech and the University of Nebraska-Lincoln, on a prototype project for the Department of Defense. They went into a lab at the University of Nebraska at Lincoln and assessed all its cyberbio-vulnerabilities. The lab develops and produces prototype vaccines, therapeutics, and prophylactic components — exactly the kind of place that you always, and especially right now, want to keep secure.
"We were creating wiki of all these nasty things."
The team found dozens of Achilles' heels, and put them in a private report. Not long after that project, the two and their colleagues wrote the paper that first used the term "cyberbiosecurity." A second paper, led by Murch, came out five months later and provided a proposed definition and more comprehensive perspective on cyberbiosecurity. But although it's now a buzzword, it's the definition, not the jargon, that matters. "Frankly, I don't really care if they call it cyberbiosecurity," says Murch. Call it what you want: Just pay attention to its tenets.
A Database of Scary Sequences
Peccoud and Murch, of course, aren't the only ones working to screen sequences and secure devices. At the nonprofit Battelle Memorial Institute in Columbus, Ohio, for instance, scientists are working on solutions that balance the openness inherent to science and the closure that can stop bad stuff. "There's a challenge there that you want to enable research but you want to make sure that what people are ordering is safe," says the organization's Neeraj Rao.
Rao can't talk about the work Battelle does for the spy agency IARPA, the Intelligence Advanced Research Projects Activity, on a project called Fun GCAT, which aims to use computational tools to deep-screen gene-sequence orders to see if they pose a threat. It can, though, talk about a twin-type internal project: ThreatSEQ (pronounced, of course, "threat seek").
The project started when "a government customer" (as usual, no one will say which) asked Battelle to curate a list of dangerous toxins and pathogens, and their genetic sequences. The researchers even started tagging sequences according to their function — like whether a particular sequence is involved in a germ's virulence or toxicity. That helps if someone is trying to use synthetic biology not to gin up a yawn-inducing old bug but to engineer a totally new one. "How do you essentially predict what the function of a novel sequence is?" says Rao. You look at what other, similar bits of code do.
"We were creating wiki of all these nasty things," says Rao. As they were working, they realized that DNA manufacturers could potentially scan in sequences that people ordered, run them against the database, and see if anything scary matched up. Kind of like that plagiarism software your college professors used.
Battelle began offering their screening capability, as ThreatSEQ. When customers -- like, currently, Twist Bioscience -- throw their sequences in, and get a report back, the manufacturers make the final decision about whether to fulfill a flagged order — whether, in the analogy, to give an F for plagiarism. After all, legitimate researchers do legitimately need to have DNA from legitimately bad organisms.
"Maybe it's the CDC," says Rao. "If things check out, oftentimes [the manufacturers] will fulfill the order." If it's your aggrieved uncle seeking the virulent pathogen, maybe not. But ultimately, no one is stopping the manufacturers from doing so.
Beyond that kind of tampering, though, cyberbiosecurity also includes keeping a lockdown on the machines that make the genetic sequences. "Somebody now doesn't need physical access to infrastructure to tamper with it," says Rao. So it needs the same cyber protections as other internet-connected devices.
Scientists are also now using DNA to store data — encoding information in its bases, rather than into a hard drive. To download the data, you sequence the DNA and read it back into a computer. But if you think like a bad guy, you'd realize that a bad guy could then, for instance, insert a computer virus into the genetic code, and when the researcher went to nab her data, her desktop would crash or infect the others on the network.
Something like that actually happened in 2017 at the USENIX security symposium, an annual programming conference: Researchers from the University of Washington encoded malware into DNA, and when the gene sequencer assembled the DNA, it corrupted the sequencer's software, then the computer that controlled it.
"This vulnerability could be just the opening an adversary needs to compromise an organization's systems," Inspirion Biosciences' J. Craig Reed and Nicolas Dunaway wrote in a paper for Frontiers in Bioengineering and Biotechnology, included in an e-book that Murch edited called Mapping the Cyberbiosecurity Enterprise.
Where We Go From Here
So what to do about all this? That's hard to say, in part because we don't know how big a current problem any of it poses. As noted in Mapping the Cyberbiosecurity Enterprise, "Information about private sector infrastructure vulnerabilities or data breaches is protected from public release by the Protected Critical Infrastructure Information (PCII) Program," if the privateers share the information with the government. "Government sector vulnerabilities or data breaches," meanwhile, "are rarely shared with the public."
"What I think is encouraging right now is the fact that we're even having this discussion."
The regulations that could rein in problems aren't as robust as many would like them to be, and much good behavior is technically voluntary — although guidelines and best practices do exist from organizations like the International Gene Synthesis Consortium and the National Institute of Standards and Technology.
Rao thinks it would be smart if grant-giving agencies like the National Institutes of Health and the National Science Foundation required any scientists who took their money to work with manufacturing companies that screen sequences. But he also still thinks we're on our way to being ahead of the curve, in terms of preventing print-your-own bioproblems: "What I think is encouraging right now is the fact that we're even having this discussion," says Rao.
Peccoud, for his part, has worked to keep such conversations going, including by doing training for the FBI and planning a workshop for students in which they imagine and work to guard against the malicious use of their research. But actually, Peccoud believes that human error, flawed lab processes, and mislabeled samples might be bigger threats than the outside ones. "Way too often, I think that people think of security as, 'Oh, there is a bad guy going after me,' and the main thing you should be worried about is yourself and errors," he says.
Murch thinks we're only at the beginning of understanding where our weak points are, and how many times they've been bruised. Decreasing those contusions, though, won't just take more secure systems. "The answer won't be technical only," he says. It'll be social, political, policy-related, and economic — a cultural revolution all its own.
Researchers Are Testing a New Stem Cell Therapy in the Hopes of Saving Millions from Blindness
Of all the infirmities of old age, failing sight is among the cruelest. It can mean the end not only of independence, but of a whole spectrum of joys—from gazing at a sunset or a grandchild's face to reading a novel or watching TV.
The Phase 1 trial will likely run through 2022, followed by a larger Phase 2 trial that could last another two or three years.
The leading cause of vision loss in people over 55 is age-related macular degeneration, or AMD, which afflicts an estimated 11 million Americans. As photoreceptors in the macula (the central part of the retina) die off, patients experience increasingly severe blurring, dimming, distortions, and blank spots in one or both eyes.
The disorder comes in two varieties, "wet" and "dry," both driven by a complex interaction of genetic, environmental, and lifestyle factors. It begins when deposits of cellular debris accumulate beneath the retinal pigment epithelium (RPE)—a layer of cells that nourish and remove waste products from the photoreceptors above them. In wet AMD, this process triggers the growth of abnormal, leaky blood vessels that damage the photoreceptors. In dry AMD, which accounts for 80 to 90 percent of cases, RPE cells atrophy, causing photoreceptors to wither away. Wet AMD can be controlled in about a quarter of patients, usually by injections of medication into the eye. For dry AMD, no effective remedy exists.
Stem Cells: Promise and Perils
Over the past decade, stem cell therapy has been widely touted as a potential treatment for AMD. The idea is to augment a patient's ailing RPE cells with healthy ones grown in the lab. A few small clinical trials have shown promising results. In a study published in 2018, for example, a University of Southern California team cultivated RPE tissue from embryonic stem cells on a plastic matrix and transplanted it into the retinas of four patients with advanced dry AMD. Because the trial was designed to test safety rather than efficacy, lead researcher Amir Kashani told a reporter, "we didn't expect that replacing RPE cells would return a significant amount of vision." Yet acuity improved substantially in one recipient, and the others regained their lost ability to focus on an object.
Therapies based on embryonic stem cells, however, have two serious drawbacks: Using fetal cell lines raises ethical issues, and such treatments require the patient to take immunosuppressant drugs (which can cause health problems of their own) to prevent rejection. That's why some experts favor a different approach—one based on induced pluripotent stem cells (iPSCs). Such cells, first produced in 2006, are made by returning adult cells to an undifferentiated state, and then using chemicals to reprogram them as desired. Treatments grown from a patient's own tissues could sidestep both hurdles associated with embryonic cells.
At least hypothetically. Today, the only stem cell therapies approved by the U.S. Food and Drug Administration (FDA) are umbilical cord-derived products for various blood and immune disorders. Although scientists are probing the use of embryonic stem cells or iPSCs for conditions ranging from diabetes to Parkinson's disease, such applications remain experimental—or fraudulent, as a growing number of patients treated at unlicensed "stem cell clinics" have painfully learned. (Some have gone blind after receiving bogus AMD therapies at those facilities.)
Last December, researchers at the National Eye Institute in Bethesda, Maryland, began enrolling patients with dry AMD in the country's first clinical trial using tissue grown from the patients' own stem cells. Led by biologist Kapil Bharti, the team intends to implant custom-made RPE cells in 12 recipients. If the effort pans out, it could someday save the sight of countless oldsters.
That, however, is what's technically referred to as a very big "if."
The First Steps
Bharti's trial is not the first in the world to use patient-derived iPSCs to treat age-related macular degeneration. In 2013, Japanese researchers implanted such cells into the eyes of a 77-year-old woman with wet AMD; after a year, her vision had stabilized, and she no longer needed injections to keep abnormal blood vessels from forming. A second patient was scheduled for surgery—but the procedure was canceled after the lab-grown RPE cells showed signs of worrisome mutations. That incident illustrates one potential problem with using stem cells: Under some circumstances, the cells or the tissue they form could turn cancerous.
"The knowledge and expertise we're gaining can be applied to many other iPSC-based therapies."
Bharti and his colleagues have gone to great lengths to avoid such outcomes. "Our process is significantly different," he told me in a phone interview. His team begins with patients' blood stem cells, which appear to be more genomically stable than the skin cells that the Japanese group used. After converting the blood cells to RPE stem cells, his team cultures them in a single layer on a biodegradable scaffold, which helps them grow in an orderly manner. "We think this material gives us a big advantage," Bharti says. The team uses a machine-learning algorithm to identify optimal cell structure and ensure quality control.
It takes about six months for a patch of iPSCs to become viable RPE cells. When they're ready, a surgeon uses a specially-designed tool to insert the tiny structure into the retina. Within days, the scaffold melts away, enabling the transplanted RPE cells to integrate fully into their new environment. Bharti's team initially tested their method on rats and pigs with eye damage mimicking AMD. The study, published in January 2019 in Science Translational Medicine, found that at ten weeks, the implanted RPE cells continued to function normally and protected neighboring photoreceptors from further deterioration. No trace of mutagenesis appeared.
Encouraged by these results, Bharti began recruiting human subjects. The Phase 1 trial will likely run through 2022, followed by a larger Phase 2 trial that could last another two or three years. FDA approval would require an even larger Phase 3 trial, with a decision expected sometime between 2025 and 2028—that is, if nothing untoward happens before then. One unknown (among many) is whether implanted cells can thrive indefinitely under the biochemically hostile conditions of an eye with AMD.
"Most people don't have a sense of just how long it takes to get something like this to work, and how many failures—even disasters—there are along the way," says Marco Zarbin, professor and chair of Ophthalmology and visual science at Rutgers New Jersey Medical School and co-editor of the book Cell-Based Therapy for Degenerative Retinal Diseases. "The first kidney transplant was done in 1933. But the first successful kidney transplant was in 1954. That gives you a sense of the time frame. We're really taking the very first steps in this direction."
Looking Ahead
Even if Bharti's method proves safe and effective, there's the question of its practicality. "My sense is that using induced pluripotent stem cells to treat the patient from whom they're derived is a very expensive undertaking," Zarbin observes. "So you'd have to have a very dramatic clinical benefit to justify that cost."
Bharti concedes that the price of iPSC therapy is likely to be high, given that each "dose" is formulated for a single individual, requires months to manufacture, and must be administered via microsurgery. Still, he expects economies of scale and production to emerge with time. "We're working on automating several steps of the process," he explains. "When that kicks in, a technician will be able to make products for 10 or 20 people at once, so the cost will drop proportionately."
Meanwhile, other researchers are pressing ahead with therapies for AMD using embryonic stem cells, which could be mass-produced to treat any patient who needs them. But should that approach eventually win FDA approval, Bharti believes there will still be room for a technique that requires neither fetal cell lines nor immunosuppression.
And not only for eye ailments. "The knowledge and expertise we're gaining can be applied to many other iPSC-based therapies," says the scientist, who is currently consulting with several companies that are developing such treatments. "I'm hopeful that we can leverage these approaches for a wide range of applications, whether it's for vision or across the body."