Scientists May Soon Be Able to Turn Off Pain with Gene Editing: Should They?
Scientists have long been aware that some people live with what's known as "congenital insensitivity to pain"—the inability to register the tingles, jolts, and aches that alert most people to injury or illness.
"If you break the chain of transmission somewhere along there, it doesn't matter what the message is—the recipient will not get it."
On the ospposite end of the spectrum, others suffer from hyperalgesia, or extreme pain; for those with erythromelalgia, also known as "Man on Fire Syndrome," warm temperatures can feel like searing heat—even wearing socks and shoes can make walking unbearable.
Strangely enough, the two conditions can be traced to mutations in the same gene, SCN9A. It produces a protein that exists in spinal cells—specifically, in the dorsal root ganglion—which transmits the sensation of pain from the nerves at the peripheral site of an injury into the central nervous system and to the brain. This fact may become the key to pain relief for the roughly 20 percent of Americans who suffer from chronic pain, and countless other patients around the world.
"If you break the chain of transmission somewhere along there, it doesn't matter what the message is—the recipient will not get it," said Dr. Fyodor Urnov, director of the Innovative Genomics Institute and a professor of molecular and cell biology at the University of California, Berkeley. "For scientists and clinicians who study this, [there's] this consistent tracking of: You break this gene, you stop feeling pain; make this gene hyperactive, you feel lots of pain—that really cuts through the correlation versus causation question."
Researchers tried for years, without much success, to find a chemical that would block that protein from working and therefore mute the pain sensation. The CRISPR-Cas9 gene editing tool could completely sidestep that approach and "turn off" pain directly.
Yet as CRISPR makes such targeted therapies increasingly possible, the ethical questions surrounding gene editing have taken on a new and more urgent cast—particularly in light of the work of the disgraced Chinese scientist He Jiankui, who announced in late 2018 that he had created the world's first genetically edited babies. He used CRISPR to edit two embryos, with the goal of disabling a gene that makes people susceptible to HIV infection; but then took the unprecedented step of implanting the edited embryos for pregnancy and birth.
Edits to germline cells, like the ones He undertook, involve alterations to gametes or embryos and carry much higher risk than somatic cell edits, since changes will be passed on to any future generations. There are also concerns that imprecise edits could result in mutations and end up causing more disorders. Recent developments, particularly the "search-and replace" prime-editing technique published last fall, will help minimize those accidental edits, but the fact remains that we have little understanding of the long-term effects of these germline edits—for the future of the patients themselves, or for the broader gene pool.
"We need to have appropriate venues where we deliberate and consider the ethical, legal and social implications of gene editing as a society."
It is much harder to predict the effects, harmful or otherwise, on the larger human population as a result of interactions with the environment or other genetic variations; with somatic cell edits, on the other hand— like the ones that would be made in an individual to turn off pain—only the person receiving the treatment is affected.
Beyond the somatic/germline distinction, there is also a larger ethical question over how much genetic interference society is willing to tolerate, which may be couched as the difference between therapeutic editing—interventions in response to a demonstrated medical need—and "enhancement" editing. The Chinese scientist He was roundly criticized in the scientific community for the fact that there are already much safer and more proven methods of preventing the parent-to-child transmission of HIV through the IVF process, making his genetic edits medically unnecessary. (The edits may also have increased the girls' risk of susceptibility to other viruses, like influenza and the West Nile virus.)
Yet there are even more extreme goals that CRISPR could be used to reach, ones further removed from any sort of medical treatment. The 1997 science fiction movie Gattaca imagined a dystopian future where genetic selection for strength and intelligence is common, creating a society that explicitly and unapologetically endorses eugenics. In the real world, Russian President Vladimir Putin has commented that genetic editing could be used to create "a genius mathematician, a brilliant musician or a soldier, a man who can fight without fear, compassion, regret or pain."
"[Such uses] would be considered using gene editing for 'enhancement,'" said Dr. Zubin Master, an associate professor of biomedical ethics at the Mayo Clinic, who noted that a series of studies have strongly suggested that members of the public, in the U.S. and around the world, are much less amenable to the prospect of gene editing for these purposes than for the treatment of illness and disease.
Putin's comments were made in 2017, before news of He's experiment broke; since then no country has moved to continue experiments on germline editing (although one Russian IVF specialist, Denis Rebrikov, appears ready to do so, if given approval). Master noted that the World Health Organization has an 18-person committee currently dedicated to considering these questions. The Expert Advisory Committee on Developing Global Standards for Governance and Oversight of Human Genome Editing first convened in March 2019; that July, it issued a recommendation to regulatory and ethics authorities in all countries to refrain from approving clinical application requests for work on human germline genome editing—the kind of alterations to genetic cells used by He. The committee's report and a fleshed-out set of guidelines is expected after its final meeting, in Geneva this September (unless the COVID-19 pandemic disrupts the timeline).
Regardless of the WHO's report, in the U.S., all regulations of new medical procedures are overseen at the federal level, subjected to extensive regulatory review by the FDA; the chance of any doctor or company going rogue is minimal to none. Likewise, the challenges we face are more on the regulatory end of the spectrum than the Gattaca end. Dr. Stephanie Malia Fullerton, a bioethics professor at the University of Washington, pointed out that eugenics not only typically involves state-sponsored control of reproduction, but requires a much more clearly delineated genetic basis of common complex traits—indeed, SCN9A is one way to get to pain, but is not the only source—and suggested that current concerns about over-prescribing opioids are a more pressing question for society to address.
In fact, Navega Therapeutics, based in San Diego, hopes to find out whether the intersection of this research into SCN9A and CRISPR would be an effective way to address the U.S. opioid crisis. Currently in a preclinical funding stage, Navega's approach focuses on editing epigenetic molecules attached to the basic DNA strand—the idea is that the gene's expression can be activated or suppressed rather than removed entirely, reducing the risk of unwanted side effects from permanently altering the genetic code.
As these studies focused on the sensation of pain go forward, what we are likely to see simultaneously is the use of CRISPR to target diseases that are the root causes of that pain. Last summer, Victoria Gray, a Mississippi woman with sickle cell disease was the second-ever person to be treated with CRISPR therapy in the U.S. The disease is caused by a genetic mutation that creates malformed blood cells, which can't carry oxygen as normal and get stuck inside blood vessels, causing debilitating pain. For the study, conducted in concert with CRISPR Therapeutics, of Cambridge, Mass., cells were removed from Gray's bone marrow, modified using CRISPR, and infused back into her body, a technique called ex vivo editing.
In early February this year, researchers at the University of Pennsylvania published a study on a first-in-human phase 1 clinical trial, in which three patients with advanced cancer received an infusion of ex vivo engineered T cells in an effort to improve antitumor immunity. The modified cells persisted for up to nine months, and the patients experienced no serious adverse side effects, suggesting that this sort of therapeutic gene editing can be performed safely and could potentially allow patients to avoid the excruciating process of chemotherapy.
Then, just this spring, researchers made another advance: The first attempt at in vivo CRISPR editing—where the edits happen inside the patient's body—is currently underway, as doctors attempt to treat a patient blinded by Leber congenital amaurosis, a rare genetic disorder. In an Oregon study sponsored by Editas Medicine and Allergan, the patient, a volunteer, was injected with a harmless virus carrying CRISPR gene-editing machinery; the hope is that the tool will be able to edit out the genetic defect and restore production of a crucial protein. Based on preliminary safety reports, the study has been cleared to continue, and data on higher doses may be available by the end of 2020. Editas Medicine and CRISPR Therapeutics are joined in this sphere by Intellia Therapeutics, which is seeking approval for a trial later this year on amyloidosis, a rare liver condition.
For any such treatment targeting SCN9A to make its way to human subjects, it would first need to undergo years' worth of testing—on mice, on primates, and then on volunteer patients after an extended informed-consent process. If everything went perfectly, Urnov estimates it could take at least three to four years end to end and cost between $5 and 10 million—but that "if" is huge.
"The idea of a regular human being, genetically pure of pain?"
And as that happens, "we need to have appropriate venues where we deliberate and consider the ethical, legal and social implications of gene editing as a society," Master said. CRISPR itself is open-source, but its application is subject to the approval of governments, institutions, and societies, which will need to figure out where to draw the line between miracle treatments and playing God. Something as unpleasant and ubiquitous as pain may in fact be the most appropriate place to start.
"The pain circuit is very old," Urnov said. "We have evolved with the senses that we have, and have become the species that we are, as a result of who we are, physiologically. Yes, I take Advil—but when I get a headache! The idea of a regular human being, genetically pure of pain?... The permanent disabling or turning down of the pain sensation, for anything other than a medical reason? … That seems to be challenging Mother Nature in the wrong ways."
In May 2022, Californian biotech Ultima Genomics announced that its UG 100 platform was capable of sequencing an entire human genome for just $100, a landmark moment in the history of the field. The announcement was particularly remarkable because few had previously heard of the company, a relative unknown in an industry long dominated by global giant Illumina which controls about 80 percent of the world’s sequencing market.
Ultima’s secret was to completely revamp many technical aspects of the way Illumina have traditionally deciphered DNA. The process usually involves first splitting the double helix DNA structure into single strands, then breaking these strands into short fragments which are laid out on a glass surface called a flow cell. When this flow cell is loaded into the sequencing machine, color-coded tags are attached to each individual base letter. A laser scans the bases individually while a camera simultaneously records the color associated with them, a process which is repeated until every single fragment has been sequenced.
Instead, Ultima has found a series of shortcuts to slash the cost and boost efficiency. “Ultima Genomics has developed a fundamentally new sequencing architecture designed to scale beyond conventional approaches,” says Josh Lauer, Ultima’s chief commercial officer.
This ‘new architecture’ is a series of subtle but highly impactful tweaks to the sequencing process ranging from replacing the costly flow cell with a silicon wafer which is both cheaper and allows more DNA to be read at once, to utilizing machine learning to convert optical data into usable information.
To put $100 genome in perspective, back in 2012 the cost of sequencing a single genome was around $10,000, a price tag which dropped to $1,000 a few years later. Before Ultima’s announcement, the cost of sequencing an individual genome was around $600.
Several studies have found that nearly 12 percent of healthy people who have their genome sequenced, then discover they have a variant pointing to a heightened risk of developing a disease that can be monitored, treated or prevented.
While Ultima’s new machine is not widely available yet, Illumina’s response has been rapid. In September 2022, the company unveiled the NovaSeq X series, which it describes as its fastest most cost-efficient sequencing platform yet, capable of sequencing genomes at $200, with further price cuts likely to follow.
But what will the rapidly tumbling cost of sequencing actually mean for medicine? “Well to start with, obviously it’s going to mean more people getting their genome sequenced,” says Michael Snyder, professor of genetics at Stanford University. “It'll be a lot more accessible to people.”
At the moment sequencing is mainly limited to certain cancer patients where it is used to inform treatment options, and individuals with undiagnosed illnesses. In the past, initiatives such as SeqFirst have attempted further widen access to genome sequencing based on growing amounts of research illustrating the potential benefits of the technology in healthcare. Several studies have found that nearly 12 percent of healthy people who have their genome sequenced, then discover they have a variant pointing to a heightened risk of developing a disease that can be monitored, treated or prevented.
“While whole genome sequencing is not yet widely used in the U.S., it has started to come into pediatric critical care settings such as newborn intensive care units,” says Professor Michael Bamshad, who heads the genetic medicine division in the University of Washington’s pediatrics department. “It is also being used more often in outpatient clinical genetics services, particularly when conventional testing fails to identify explanatory variants.”
But the cost of sequencing itself is only one part of the price tag. The subsequent clinical interpretation and genetic counselling services often come to several thousand dollars, a cost which insurers are not always willing to pay.
As a result, while Bamshad and others hope that the arrival of the $100 genome will create new opportunities to use genetic testing in innovative ways, the most immediate benefits are likely to come in the realm of research.
Bigger Data
There are numerous ways in which cheaper sequencing is likely to advance scientific research, for example the ability to collect data on much larger patient groups. This will be a major boon to scientists working on complex heterogeneous diseases such as schizophrenia or depression where there are many genes involved which all exert subtle effects, as well as substantial variance across the patient population. Bigger studies could help scientists identify subgroups of patients where the disease appears to be driven by similar gene variants, who can then be more precisely targeted with specific drugs.
If insurers can figure out the economics, Snyder even foresees a future where at a certain age, all of us can qualify for annual sequencing of our blood cells to search for early signs of cancer or the potential onset of other diseases like type 2 diabetes.
David Curtis, a genetics professor at University College London, says that scientists studying these illnesses have previously been forced to rely on genome-wide association studies which are limited because they only identify common gene variants. “We might see a significant increase in the number of large association studies using sequence data,” he says. “It would be far preferable to use this because it provides information about rare, potentially functional variants.”
Cheaper sequencing will also aid researchers working on diseases which have traditionally been underfunded. Bamshad cites cystic fibrosis, a condition which affects around 40,000 children and adults in the U.S., as one particularly pertinent example.
“Funds for gene discovery for rare diseases are very limited,” he says. “We’re one of three sites that did whole genome sequencing on 5,500 people with cystic fibrosis, but our statistical power is limited. A $100 genome would make it much more feasible to sequence everyone in the U.S. with cystic fibrosis and make it more likely that we discover novel risk factors and pathways influencing clinical outcomes.”
For progressive diseases that are more common like cancer and type 2 diabetes, as well as neurodegenerative conditions like multiple sclerosis and ALS, geneticists will be able to go even further and afford to sequence individual tumor cells or neurons at different time points. This will enable them to analyze how individual DNA modifications like methylation, change as the disease develops.
In the case of cancer, this could help scientists understand how tumors evolve to evade treatments. Within in a clinical setting, the ability to sequence not just one, but many different cells across a patient’s tumor could point to the combination of treatments which offer the best chance of eradicating the entire cancer.
“What happens at the moment with a solid tumor is you treat with one drug, and maybe 80 percent of that tumor is susceptible to that drug,” says Neil Ward, vice president and general manager in the EMEA region for genomics company PacBio. “But the other 20 percent of the tumor has already got mutations that make it resistant, which is probably why a lot of modern therapies extend life for sadly only a matter of months rather than curing, because they treat a big percentage of the tumor, but not the whole thing. So going forwards, I think that we will see genomics play a huge role in cancer treatments, through using multiple modalities to treat someone's cancer.”
If insurers can figure out the economics, Snyder even foresees a future where at a certain age, all of us can qualify for annual sequencing of our blood cells to search for early signs of cancer or the potential onset of other diseases like type 2 diabetes.
“There are companies already working on looking for cancer signatures in methylated DNA,” he says. “If it was determined that you had early stage cancer, pre-symptomatically, that could then be validated with targeted MRI, followed by surgery or chemotherapy. It makes a big difference catching cancer early. If there were signs of type 2 diabetes, you could start taking steps to mitigate your glucose rise, and possibly prevent it or at least delay the onset.”
This would already revolutionize the way we seek to prevent a whole range of illnesses, but others feel that the $100 genome could also usher in even more powerful and controversial preventative medicine schemes.
Newborn screening
In the eyes of Kári Stefánsson, the Icelandic neurologist who been a visionary for so many advances in the field of human genetics over the last 25 years, the falling cost of sequencing means it will be feasible to sequence the genomes of every baby born.
“We have recently done an analysis of genomes in Iceland and the UK Biobank, and in 4 percent of people you find mutations that lead to serious disease, that can be prevented or dealt with,” says Stefansson, CEO of deCODE genetics, a subsidiary of the pharmaceutical company Amgen. “This could transform our healthcare systems.”
As well as identifying newborns with rare diseases, this kind of genomic information could be used to compute a person’s risk score for developing chronic illnesses later in life. If for example, they have a higher than average risk of colon or breast cancer, they could be pre-emptively scheduled for annual colonoscopies or mammograms as soon as they hit adulthood.
To a limited extent, this is already happening. In the UK, Genomics England has launched the Newborn Genomes Programme, which plans to undertake whole-genome sequencing of up to 200,000 newborn babies, with the aim of enabling the early identification of rare genetic diseases.
"I have not had my own genome sequenced and I would not have wanted my parents to have agreed to this," Curtis says. "I don’t see that sequencing children for the sake of some vague, ill-defined benefits could ever be justifiable.”
However, some scientists feel that it is tricky to justify sequencing the genomes of apparently healthy babies, given the data privacy issues involved. They point out that we still know too little about the links which can be drawn between genetic information at birth, and risk of chronic illness later in life.
“I think there are very difficult ethical issues involved in sequencing children if there are no clear and immediate clinical benefits,” says Curtis. “They cannot consent to this process. I have not had my own genome sequenced and I would not have wanted my parents to have agreed to this. I don’t see that sequencing children for the sake of some vague, ill-defined benefits could ever be justifiable.”
Curtis points out that there are many inherent risks about this data being available. It may fall into the hands of insurance companies, and it could even be used by governments for surveillance purposes.
“Genetic sequence data is very useful indeed for forensic purposes. Its full potential has yet to be realized but identifying rare variants could provide a quick and easy way to find relatives of a perpetrator,” he says. “If large numbers of people had been sequenced in a healthcare system then it could be difficult for a future government to resist the temptation to use this as a resource to investigate serious crimes.”
While sequencing becoming more widely available will present difficult ethical and moral challenges, it will offer many benefits for society as a whole. Cheaper sequencing will help boost the diversity of genomic datasets which have traditionally been skewed towards individuals of white, European descent, meaning that much of the actionable medical information which has come out of these studies is not relevant to people of other ethnicities.
Ward predicts that in the coming years, the growing amount of genetic information will ultimately change the outcomes for many with rare, previously incurable illnesses.
“If you're the parent of a child that has a susceptible or a suspected rare genetic disease, their genome will get sequenced, and while sadly that doesn’t always lead to treatments, it’s building up a knowledge base so companies can spring up and target that niche of a disease,” he says. “As a result there’s a whole tidal wave of new therapies that are going to come to market over the next five years, as the genetic tools we have, mature and evolve.”
This article was first published by Leaps.org in October 2022.
The livestock trucks arrived all night. One after the other they backed up to the wood chute leading to a dusty corral and loosed their cargo — 580 head of cattle by the time the last truck pulled away at 3pm the next afternoon. Dan Probert, astride his horse, guided the cows to paddocks of pristine grassland stretching alongside the snow-peaked Wallowa Mountains. They’d spend the summer here grazing bunchgrass and clovers and biscuitroot. The scuffle of their hooves and nibbles of their teeth would mimic the elk, antelope and bison that are thought to have historically roamed this portion of northeastern Oregon’s Zumwalt Prairie, helping grasses grow and restoring health to the soil.
The cows weren’t Probert’s, although the fifth-generation rancher and one other member of the Carman Ranch Direct grass-fed beef collective also raise their own herds here for part of every year. But in spring, when the prairie is in bloom, Probert receives cattle from several other ranchers. As the grasses wither in October, the cows move on to graze fertile pastures throughout the Columbia Basin, which stretches across several Pacific Northwest states; some overwinter on a vegetable farm in central Washington, feeding on corn leaves and pea vines left behind after harvest.
Sharing land and other resources among farmers isn’t new. But research shows it may be increasingly relevant in a time of climatic upheaval, potentially influencing “farmers to adopt environmentally friendly practices and agricultural innovation,” according to a 2021 paper in the Journal of Economic Surveys. Farmers might share knowledge about reducing pesticide use, says Heather Frambach, a supply chain consultant who works with farmers in California and elsewhere. As a group they may better qualify for grants to monitor soil and water quality.
Most research around such practices applies to cooperatives, whose owner-members equally share governance and profits. But a collective like Carman Ranch’s — spearheaded by fourth-generation rancher Cory Carman, who purchases beef from eight other ranchers to sell under one “regeneratively” certified brand — shows when producers band together, they can achieve eco-benefits that would be elusive if they worked alone.
Vitamins and minerals in soil pass into plants through their roots, then into cattle as they graze, then back around as the cows walk around pooping.
Carman knows from experience. Taking over her family's land in 2003, she started selling grass-fed beef “because I really wanted to figure out how to not participate in the feedlot world, to have a healthier product. I didn't know how we were going to survive,” she says. Part of her land sits on a degraded portion of Zumwalt Prairie replete with invasive grasses; working to restore it, she thought, “What good does it do to kill myself trying to make this ranch more functional? If you want to make a difference, change has to be more than single entrepreneurs on single pieces of land. It has to happen at a community level.” The seeds of her collective were sown.
Raising 100 percent grass-fed beef requires land that’s got something for cows to graze in every season — which most collective members can’t access individually. So, they move cattle around their various parcels. It’s practical, but it also restores nutrient flows “to the way they used to move, from lowlands and canyons during the winter to higher-up places as the weather gets hot,” Carman says. Meaning, vitamins and minerals in soil pass into plants through their roots, then into cattle as they graze, then back around as the cows walk around pooping.
Cory Carman sells grass-fed beef, which requires land that’s got something for cows to graze in every season.
Courtesy Cory Carman
Each collective member has individual ecological goals: Carman brought in pigs to root out invasive grasses and help natives flourish. Probert also heads a more conventional grain-finished beef collective with 100 members, and their combined 6.5 million ranchland acres were eligible for a grant supporting climate-friendly practices, which compels them to improve soil and water health and biodiversity and make their product “as environmentally friendly as possible,” Probert says. The Washington veg farmer reduced tilling and pesticide use thanks to the ecoservices of visiting cows. Similarly, a conventional hay farmer near Carman has reduced his reliance on fertilizer by letting cattle graze the cover crops he plants on 80 acres.
Additionally, the collective must meet the regenerative standards promised on their label — another way in which they work together to achieve ecological goals. Says David LeZaks, formerly a senior fellow at finance-focused ecology nonprofit Croatan Institute, it’s hard for individual farmers to access monetary assistance. “But it's easier to get financing flowing when you increase the scale with cooperatives or collectives,” he says. “This supports producers in ways that can lead to better outcomes on the landscape.”
New, smaller scale farmers might gain the most from collective and cooperative models.
For example, it can help them minimize waste by using more of an animal, something our frugal ancestors excelled at. Small-scale beef producers normally throw out hides; Thousand Hills’ 50 regenerative beef producers together have enough to sell to Timberland to make carbon-neutral leather. In another example, working collectively resulted in the support of more diverse farms: Meadowlark Community Mill in Wisconsin went from working with one wheat grower, to sourcing from several organic wheat growers marketing flour under one premium brand.
Another example shows how these collaborations can foster greater equity, among other benefits: The Federation of Southern Cooperatives has a mission to support Black farmers as they build community health. It owns several hundred forest acres in Alabama, where it teaches members to steward their own forest land and use it to grow food — one member coop raises goats to graze forest debris and produce milk. Adding the combined acres of member forest land to the Federation’s, the group qualified for a federal conservation grant that will keep this resource available for food production, and community environmental and mental health benefits. “That's the value-add of the collective land-owner structure,” says Dãnia Davy, director of land retention and advocacy.
New, smaller scale farmers might gain the most from collective and cooperative models, says Jordan Treakle, national program coordinator of the National Family Farm Coalition (NFFC). Many of them enter farming specifically to raise healthy food in healthy ways — with organic production, or livestock for soil fertility. With land, equipment and labor prohibitively expensive, farming collectively allows shared costs and risk that buy farmers the time necessary to “build soil fertility and become competitive” in the marketplace, Treakle says. Just keeping them in business is an eco-win; when small farms fail, they tend to get sold for development or absorbed into less-diversified operations, so the effects of their success can “reverberate through the entire local economy.”
Frambach, the supply chain consultant, has been experimenting with what she calls “collaborative crop planning,” where she helps farmers strategize what they’ll plant as a group. “A lot of them grow based on what they hear their neighbor is going to do, and that causes really poor outcomes,” she says. “Nobody replanted cauliflower after the [atmospheric rivers in California] this year and now there's a huge shortage of cauliflower.” A group plan can avoid the under-planting that causes farmers to lose out on revenue.
It helps avoid overplanted crops, too, which small farmers might have to plow under or compost. Larger farmers, conversely, can sell surplus produce into the upcycling market — to Matriark Foods, for example, which turns it into value-add products like pasta sauce for companies like Sysco that supply institutional kitchens at colleges and hospitals. Frambach and Anna Hammond, Matriark’s CEO, want to collectivize smaller farmers so that they can sell to the likes of Matriark and “not lose an incredible amount of income,” Hammond says.
Ultimately, farming is fraught with challenges and even collectivizing doesn’t guarantee that farms will stay in business. But with agriculture accounting for almost 30 percent of greenhouse gas emissions globally, there's an “urgent” need to shift farming practices to more environmentally sustainable models, as well as a “demand in the marketplace for it,” says NFFC’s Treakle. “The growth of cooperative and collective farming can be a huge, huge boon for the ecological integrity of the system.”