Body-on-a-chip, prime editing, and gut microbes all are poised to make a big impact in 2020.
1. Happening Now: Body-on-a-Chip Technology Is Enabling Safer Drug Trials and Better Cancer Research
Researchers have increasingly used the technology known as "lab-on-a-chip" or "organ-on-a-chip" to test the effects of pharmaceuticals, toxins, and chemicals on humans. Rather than testing on animals, which raises ethical concerns and can sometimes be inaccurate, and human-based clinical trials, which can be expensive and difficult to iterate, scientists turn to tiny, micro-engineered chips—about the size of a thumb drive.
It's possible that doctors could one day take individual cell samples and create personalized treatments, testing out any medications on the chip.
The chips are lined with living samples of human cells, which mimic the physiology and mechanical forces experienced by cells inside the human body, down to blood flow and breathing motions; the functions of organs ranging from kidneys and lungs to skin, eyes, and the blood-brain barrier.
A more recent—and potentially even more useful—development takes organ-on-a-chip technology to the next level by integrating several chips into a "body-on-a-chip." Since human organs don't work in isolation, seeing how they all react—and interact—once a foreign element has been introduced can be crucial to understanding how a certain treatment will or won't perform. Dr. Shyni Varghese, a MEDx investigator at the Duke University School of Medicine, is one of the researchers working with these systems in order to gain a more nuanced understanding of how multiple different organs react to the same stimuli.
Her lab is working on "tumor-on-a-chip" models, which can not only show the progression and treatment of cancer, but also model how other organs would react to immunotherapy and other drugs. "The effect of drugs on different organs can be tested to identify potential side effects," Varghese says. In addition, these models can help the researchers figure out how cancers grow and spread, as well as how to effectively encourage immune cells to move in and attack a tumor.
One body-on-a-chip used by Dr. Varghese's lab tracks the interactions of five organs—brain, heart, liver, muscle, and bone.
As their research progresses, Varghese and her team are looking for ways to maintain the long-term function of the engineered organs. In addition, she notes that this kind of research is not just useful for generalized testing; "organ-on-chip technologies allow patient-specific analyses, which can be used towards a fundamental understanding of disease progression," Varghese says. It's possible that doctors could one day take individual cell samples and create personalized treatments, testing out any medications on the chip for safety, efficacy, and potential side effects before writing a prescription.
2. Happening Soon: Prime Editing Will Have the Power to "Find and Replace" Disease-Causing Genes
Biochemist David Liu made industry-wide news last fall when he and his lab at MIT's Broad Institute, led by Andrew Anzalone, published a paper on prime editing: a new, more focused technology for editing genes. Prime editing is a descendant of the CRISPR-Cas9 system that researchers have been working with for years, and a cousin to Liu's previous innovation—base editing, which can make a limited number of changes to a single DNA letter at a time.
By contrast, prime editing has the potential to make much larger insertions and deletions; it also doesn't require the tweaked cells to divide in order to write the changes into the DNA, which could make it especially suitable for central nervous system diseases, like Parkinson's.
Crucially, the prime editing technique has a much higher efficiency rate than the older CRISPR system, and a much lower incidence of accidental insertions or deletions, which can make dangerous changes for a patient.
It also has a very broad potential range: according to Liu, 89% of the pathogenic mutations that have been collected in ClinVar (a public archive of human variations) could, in principle, be treated with prime editing—although he is careful to note that correcting a single genetic mutation may not be sufficient to fully treat a genetic disease.
Figuring out just how prime editing can be used most effectively and safely will be a long process, but it's already underway. The same day that Liu and his team posted their paper, they also made the basic prime editing constructs available for researchers around the world through Addgene, a plasmid repository, so that others in the scientific community can test out the technique for themselves. It might be years before human patients will see the results, and in the meantime, significant bioethical questions remain about the limits and sociological effects of such a powerful gene-editing tool. But in the long fight against genetic diseases, it's a huge step forward.
3. Happening When We Fund It: Focusing on Microbiome Health Could Help Us Tackle Social Inequality—And Vice Versa
The past decade has seen a growing awareness of the major role that the microbiome, the microbes present in our digestive tract, play in human health. Having a less-healthy microbiome is correlated with health risks like diabetes and depression, and interventions that target gut health, ranging from kombucha to fecal transplants, have cropped up with increasing frequency.
New research from the University of Maine's Dr. Suzanne Ishaq takes an even broader view, arguing that low-income and disadvantaged populations are less likely to have healthy, diverse gut bacteria, and that increasing access to beneficial microorganisms is an important juncture of social justice and public health.
"Basically, allowing people to lead healthy lives allows them to access and recruit microbes."
"Typically, having a more diverse bacterial community is associated with health, and having fewer different species is associated with illness and may leave you open to infection from bacteria that are good at exploiting opportunities," Ishaq says.
Having a healthy biome doesn't mean meeting one fixed ratio of gut bacteria, since different combinations of microbes can generate roughly similar results when they work in concert. Generally, "good" microbes are the ones that break down fiber and create the byproducts that we use for energy, or ones like lactic acid bacteria that work to make microbials and keep other bacteria in check. The microbial universe in your gut is chaotic, Ishaq says. "Microbes in your gut interact with each other, with you, with your food, or maybe they don't interact at all and pass right through you." Overall, it's tricky to name specific microbial communities that will make or break someone's health.
There are important corollaries between environment and biome health, though, which Ishaq points out: Living in urban environments reduces microbial exposure, and losing the microorganisms that humans typically source from soil and plants can reduce our adaptive immunity and ability to fight off conditions like allergies and asthma. Access to green space within cities can counteract those effects, but in the U.S. that access varies along income, education, and racial lines. Likewise, lower-income communities are more likely to live in food deserts or areas where the cheapest, most convenient food options are monotonous and low in fiber, further reducing microbial diversity.
Ishaq also suggests other areas that would benefit from further study, like the correlation between paid family leave, breastfeeding, and gut microbiota. There are technical and ethical challenges to direct experimentation with human populations—but that's not what Ishaq sees as the main impediment to future research.
"The biggest roadblock is money, and the solution is also money," she says. "Basically, allowing people to lead healthy lives allows them to access and recruit microbes."
That means investment in things we already understand to improve public health, like better education and healthcare, green space, and nutritious food. It also means funding ambitious, interdisciplinary research that will investigate the connections between urban infrastructure, housing policy, social equity, and the millions of microbes keeping us company day in and day out.
Recent advancements in engineering mean that the first preclinical trials for an artificial kidney could happen soon.
Still, the devices aren’t ready for testing in humans—yet. But recent advancements in engineering mean that the first preclinical trials for an artificial kidney could happen soon, according to Jonathan Himmelfarb, a nephrologist at the University of Washington.
“It would liberate people with kidney failure,” Himmelfarb says.
An engineering marvel
Compared to the heart or the brain, the kidney doesn’t get as much respect from the medical profession, but its job is far more complex. “It does hundreds of different things,” says UCLA’s Ira Kurtz.
Kurtz would know. He’s worked as a nephrologist for 37 years, devoting his career to helping those with kidney disease. While his colleagues in cardiology and endocrinology have seen major advances in the development of artificial hearts and insulin pumps, little has changed for patients on hemodialysis. The machines remain bulky and require large volumes of a liquid called dialysate to remove toxins from a patient’s blood, along with gallons of purified water. A kidney transplant is the next best thing to someone’s own, functioning organ, but with over 600,000 Americans on dialysis and only about 100,000 kidney transplants each year, most of those in kidney failure are stuck on dialysis.
Part of the lack of progress in artificial kidney design is the sheer complexity of the kidney’s job. Each of the 45 different cell types in the kidney do something different.
Part of the lack of progress in artificial kidney design is the sheer complexity of the kidney’s job. To build an artificial heart, Kurtz says, you basically need to engineer a pump. An artificial pancreas needs to balance blood sugar levels with insulin secretion. While neither of these tasks is simple, they are fairly straightforward. The kidney, on the other hand, does more than get rid of waste products like urea and other toxins. Each of the 45 different cell types in the kidney do something different, helping to regulate electrolytes like sodium, potassium, and phosphorous; maintaining blood pressure and water balance; guiding the body’s hormonal and inflammatory responses; and aiding in the formation of red blood cells.
There's been little progress for patients during Ira Kurtz's 37 years as a nephrologist. Artificial kidneys would change that.
UCLA
Dialysis primarily filters waste, and does so well enough to keep someone alive, but it isn’t a true artificial kidney because it doesn’t perform the kidney’s other jobs, according to Kurtz, such as sensing levels of toxins, wastes, and electrolytes in the blood. Due to the size and water requirements of existing dialysis machines, the equipment isn’t portable. Physicians write a prescription for a certain duration of dialysis and assess how well it’s working with semi-regular blood tests. The process of dialysis itself, however, is conducted blind. Doctors can’t tell how much dialysis a patient needs based on kidney values at the time of treatment, says Meera Harhay, a nephrologist at Drexel University in Philadelphia.
But it’s the impact of dialysis on their day-to-day lives that creates the most problems for patients. Only one-quarter of those on dialysis are able to remain employed (compared to 85% of similar-aged adults), and many report a low quality of life. Having more flexibility in life would make a major different to her patients, Harhay says.
“Almost half their week is taken up by the burden of their treatment. It really eats away at their freedom and their ability to do things that add value to their life,” she says.
Art imitates life
The challenge for artificial kidney designers was how to compress the kidney’s natural functions into a portable, wearable, or implantable device that wouldn’t need constant access to gallons of purified and sterilized water. The other universal challenge they faced was ensuring that any part of the artificial kidney that would come in contact with blood was kept germ-free to prevent infection.
As part of the 2021 KidneyX Prize, a partnership between the U.S. Department of Health and Human Services and the American Society of Nephrology, inventors were challenged to create prototypes for artificial kidneys. Himmelfarb’s team at the University of Washington’s Center for Dialysis Innovation won the prize by focusing on miniaturizing existing technologies to create a portable dialysis machine. The backpack sized AKTIV device (Ambulatory Kidney to Increase Vitality) will recycle dialysate in a closed loop system that removes urea from blood and uses light-based chemical reactions to convert the urea to nitrogen and carbon dioxide, which allows the dialysate to be recirculated.
Himmelfarb says that the AKTIV can be used when at home, work, or traveling, which will give users more flexibility and freedom. “If you had a 30-pound device that you could put in the overhead bins when traveling, you could go visit your grandkids,” he says.
Kurtz’s team at UCLA partnered with the U.S. Kidney Research Corporation and Arkansas University to develop a dialysate-free desktop device (about the size of a small printer) as the first phase of a progression that will he hopes will lead to something small and implantable. Part of the reason for the artificial kidney’s size, Kurtz says, is the number of functions his team are cramming into it. Not only will it filter urea from blood, but it will also use electricity to help regulate electrolyte levels in a process called electrodeionization. Kurtz emphasizes that these additional functions are what makes his design a true artificial kidney instead of just a small dialysis machine.
One version of an artificial kidney.
UCLA
“It doesn't have just a static function. It has a bank of sensors that measure chemicals in the blood and feeds that information back to the device,” Kurtz says.
Other startups are getting in on the game. Nephria Bio, a spinout from the South Korean-based EOFlow, is working to develop a wearable dialysis device, akin to an insulin pump, that uses miniature cartridges with nanomaterial filters to clean blood (Harhay is a scientific advisor to Nephria). Ian Welsford, Nephria’s co-founder and CTO, says that the device’s design means that it can also be used to treat acute kidney injuries in resource-limited settings. These potentials have garnered interest and investment in artificial kidneys from the U.S. Department of Defense.
For his part, Burton is most interested in an implantable device, as that would give him the most freedom. Even having a regular outpatient procedure to change batteries or filters would be a minor inconvenience to him.
“Being plugged into a machine, that’s not mimicking life,” he says.
This article was first published by Leaps.org on May 5, 2022.
New research focuses on methods that could change medicine-making worldwide. The scientists propose bursting cells open, removing their DNA and using the cellular gears inside to make therapies.
Rao and his team of collaborators, which spans multiple research institutions, believe they have a better approach that may change medicine-making worldwide. They suggest forgoing the concept of using living cells as medicine-producers. Instead, they propose breaking the cells and using the remaining cellular gears for assembling the therapeutic compounds. Instead of inserting the DNA into living cells, the team burst them open, and removed their DNA altogether. Yet, the residual molecular machinery of ribosomes, polymerases and other cogwheels still functioned the way it would in a cell. “Now if you drop your DNA drug-making instructions into that soup, this machinery starts making what you need,” Rao explains. “And because you're no longer worrying about living cells, it becomes much simpler and more efficient.” The collaborators detail their cell-free protein synthesis or CFPS method in their recent paper published in preprint BioAxiv.
While CFPS does not use living cells, it still needs the basic building blocks to assemble proteins from—such as amino acids, nucleotides and certain types of enzymes. These are regularly added into this “soup” to keep the molecular factory chugging. “We just mix everything in as a batch and we let it integrate,” says James Robert Swartz, professor of chemical engineering and bioengineering at Stanford University and co-author of the paper. “And we make sure that we provide enough oxygen.” Rao likens the process to making milk from milk powder.
For a variety of reasons—from the field’s general inertia to regulatory approval hurdles—the method hasn’t become mainstream. The pandemic rekindled interest in medicines that can be made quickly and easily, so it drew more attention to the technology.
The idea of a cell-free protein synthesis is older than one might think. Swartz first experimented with it around 1997, when he was a chemical engineer at Genentech. While working on engineering bacteria to make pharmaceuticals, he discovered that there was a limit to what E. coli cells, the workhorse darling of pharma, could do. For example, it couldn’t grow and properly fold some complex proteins. “We tried many genetic engineering approaches, many fermentation, development, and environmental control approaches,” Swartz recalls—to no avail.
“The organism had its own agenda,” he quips. “And because everything was happening within the organism, we just couldn't really change those conditions very easily. Some of them we couldn’t change at all—we didn’t have control.”
It was out of frustration with the defiant bacteria that a new idea took hold. Could the cells be opened instead, so that the protein-forming reactions could be influenced more easily? “Obviously, we’d lose the ability for them to reproduce,” Swartz says. But that also meant that they no longer needed to keep the cells alive and could focus on making the specific reactions happen. “We could take the catalysts, the enzymes, and the more complex catalysts and activate them, make them work together, much as they would in a living cell, but the way we wanted.”
In 1998, Swartz joined Stanford, and began perfecting the biochemistry of the cell-free method, identifying the reactions he wanted to foster and stopping those he didn’t want. He managed to make the idea work, but for a variety of reasons—from the field’s general inertia to regulatory approval hurdles—the method hasn’t become mainstream. The pandemic rekindled interest in medicines that can be made quickly and easily, so it drew more attention to the technology. For their BioArxiv paper, the team tested the method by growing a specific antiviral protein called griffithsin.
First identified by Barry O’Keefe at National Cancer Institute over a decade ago, griffithsin is an antiviral known to interfere with many viruses’ ability to enter cells—including HIV, SARS, SARS-CoV-2, MERS and others. Originally isolated from the red algae Griffithsia, it works differently from antibodies and antibody cocktails.
Most antiviral medicines tend to target the specific receptors that viruses use to gain entry to the cells they infect. For example, SARS-CoV-2 uses the infamous spike protein to latch onto the ACE2 receptor of mammalian cells. The antibodies or other antiviral molecules stick to the spike protein, shutting off its ability to cling onto the ACE2 receptors. Unfortunately, the spike proteins mutate very often, so the medicines lose their potency. On the contrary, griffithsin has the ability to cling to the different parts of viral shells called capsids—namely to the molecules of mannose, a type of sugar. That extra stuff, glued all around the capsid like dead weight, makes it impossible for the virus to squeeze into the cell.
“Every time we have a vaccine or an antibody against a specific SARS-CoV-2 strain, that strain then mutates and so you lose efficacy,” Rao explains. “But griffithsin molecules glom onto the viral capsid, so the capsid essentially becomes a sticky mess and can’t enter the cell.” Mannose molecules also don’t mutate as easily as viruses’ receptors, so griffithsin-based antivirals do not have to be constantly updated. And because mannose molecules are found on many viruses’ capsids, it makes griffithsin “a universal neutralizer,” Rao explains.
“When griffithsin was discovered, we recognized that it held a lot of promise as a potential antiviral agent,” O’Keefe says. In 2010, he published a paper about griffithsin efficacy in neutralizing viruses of the corona family—after the first SARS outbreak in the early 2000s, the scientific community was interested in such antivirals. Yet, griffithsin is still not available as an off-the-shelf product. So during the Covid pandemic, the team experimented with synthesizing griffithsin using the cell-free production method. They were able to generate potent griffithsin in less than 24 hours without having to grow living cells.
The antiviral protein isn't the only type of medicine that can be made cell-free. The proteins needed for vaccine production could also be made the same way. “Such portable, on-demand drug manufacturing platforms can produce antiviral proteins within hours, making them ideal for combating future pandemics,” Rao says. “We would be able to stop the pandemic before it spreads.”
Top: Describes the process used in the study. Bottom: Describes how the new medicines and vaccines could be made at the site of a future viral outbreak.
Image courtesy of Rao and team, sourced from An approach to rapid distributed manufacturing of broad spectrumanti-viral griffithsin using cell-free systems to mitigate pandemics.
Rao’s idea is to perfect the technology to the point that any hospital or pharmacy can load up the media containing molecular factories, mix up the required amino acids, nucleotides and enzymes, and harvest the meds within hours. That will allow making medicines onsite and on demand. “That would be a self-contained production unit, so that you could just ship the production wherever the pandemic is breaking out,” says Swartz.
These units and the meds they produce, will, of course, have to undergo rigorous testing. “The biggest hurdles will be validating these against conventional technology,” Rao says. The biotech industry is risk-averse and prefers the familiar methods. But if this approach works, it may go beyond emergency situations and revolutionize the medicine-making paradigm even outside hospitals and pharmacies. Rao hopes that someday the method might become so mainstream that people may be able to buy and operate such reactors at home. “You can imagine a diabetic patient making insulin that way, or some other drugs,” Rao says. It would work not unlike making baby formula from the mere white powder. Just add water—and some oxygen, too.