I guess if you’re going to use bacteria as part of your gene editing technology (CRISPR [clustered regularly interspaced short palindromic repeats]/Cas9) then, you might half expect the body’s immune system may have developed some defenses. A Jan. 9, 2018 article by Sarah Zhang for The Atlantic provides some insight into what the new research suggests (Note: Links have been removed),
2018 is supposed to be the year of CRISPR in humans. The first U.S. and European clinical trials that test the gene-editing tool’s ability to treat diseases—such as sickle-cell anemia, beta thalassemia, and a type of inherited blindness—are slated to begin this year.
But the year has begun on a cautionary note. On Friday [January 5, 2018], Stanford researchers posted a preprint (which has not been peer reviewed) to the website biorXiv highlighting a potential obstacle to using CRISPR in humans: Many of us may already be immune to it. That’s because CRISPR actually comes from bacteria that often live on or infect humans, and we have built up immunity to the proteins from these bacteria over our lives.
Not all CRISPR therapies in humans will be doomed. “We don’t think this is the end of the story. This is the start of the story,” says Porteus [Matthew Porteus, a pediatrician and stem-cell researcher at Stanford]. There are likely ways around the problem of immunity to CRISPR proteins, and many of the early clinical trials appear to be designed around this problem.
Porteus and his colleagues focused on two versions of Cas9, the bacterial protein mostly commonly used in CRISPR gene editing. One comes from Staphylococcus aureus, which often harmlessly lives on skin but can sometimes causes staph infections, and another from Streptococcus pyogenes, which causes strep throat but can also become “flesh-eating bacteria” when it spreads to other parts of the body. So yeah, you want your immune system to be on guard against these bacteria.
The human immune system has a couple different ways of recognizing foreign proteins, and the team tested for both. First, they looked to see if people have molecules in their blood called antibodies that can specifically bind to Cas9. Among 34 people they tested, 79 percent had antibodies against the staph Cas9 and 65 percent against the strep Cas9.
The Stanford team only tested for preexisting immunity against Cas9, but anytime you inject a large bacterial protein into the human body, it can provoke an immune response. After all, that’s how the immune system learns to fight off bacteria it’s never seen before. (Preexisting immunity can make the response faster and more robust, though.)
The danger of the immune system turning on a patient’s body hangs over a lot of research into correcting genes. In the late 1990s and 2000s, research into gene therapy was derailed by the death of 18-year-old Jesse Gelsinger, who died from an immune reaction to the virus used to deliver the corrected gene. This is the worst-case scenario that the CRISPR world hopes to avoid.
This year could be a defining one for CRISPR, the gene editing technique, which has been hailed as an important breakthrough in laboratory research. That’s because the first company-sponsored clinical studies will be conducted to see if it can help treat diseases in humans, according to an article in Chemical & Engineering News (C&EN), the weekly newsmagazine of the American Chemical Society.
C&EN Assistant Editor Ryan Cross reports that a big push is coming from industry, specifically from three companies that are each partly founded by one of the three inventors of the method. They are zeroing in on the blood diseases called sickle-cell anemia and β-thalassemia, mostly because their precise cause is known. In these diseases, hemoglobin doesn’t function properly, leading to severe health issues in some people. Crispr Therapeutics and Intellia Therapeutics plan to test the technique to boost levels of an alternative version of healthy hemoglobin. Editas Medicine, however, will also use CRISPR to correct mutations in the faulty hemoglobin gene. Labs led by university researchers are also joining the mix, starting or continuing clinical trials with the approach in 2018.
Because CRISPR is being used to cut a cell’s DNA and insert a new sequence, concerns have been raised about the potential for accidents. A cut in the wrong place could mean introducing a new mutation that could be benign — or cancerous. But according to proponents of the method, researchers are conducting extensive computer predictions and in vitro tests to help avoid this outcome.
The January 8, 2018 Chemical and Engineering News (C&EN) open access article by Ryan Cross is here.
Finally, if you are interested in how this affects research as it’s being developed, there’s University of British Columbia researcher Rosie Redfield’s January 16, 2018 posting on RRResearch blog,
Thursday’s [January 11, 2018] post described the hypothesis that bacteria might use gene transfer agent particles to inoculate other cells in the population with fragments of phage DNA, and outlined an experiment to test this. Now I’m realizing that I need to know a lot more about the kind of immunity I should expect to see if this GTA-as-vaccine hypothesis is correct.
That should give you some idea of what I meant by “research as it’s being developed.” Redfield’s blog is not for the mildly interested.
Redfield is well-known internationally as being one of the first to refute research which suggested the existence of an ‘arsenic bacterium’ (see my Dec. 8, 2010 posting: My apologies for arsenic blooper. She’s first mentioned in the second excerpt, second paragraph.) The affair was known online as #arseniclife. There’s a May 27, 2011 essay by Carl Zimmer on Slate titled: The Discovery of Arsenic-Based Twitter: How #arseniclife changed science.
It must have been quite the conference. Josiah Zayner plunged a needle into himself and claimed to have changed his DNA (deoxyribonucleic acid) while giving his talk. (*Segue: There is some Canadian content if you keep reading.*) From an Oct. 10, 2017 article by Adele Peters for Fast Company (Note: A link has been removed),
“What we’ve got here is some DNA, and this is a syringe,” Josiah Zayner tells a room full of synthetic biologists and other researchers. He fills the needle and plunges it into his skin. “This will modify my muscle genes and give me bigger muscles.”
Zayner, a biohacker–basically meaning he experiments with biology in a DIY lab rather than a traditional one–was giving a talk called “A Step-by-Step Guide to Genetically Modifying Yourself With CRISPR” at the SynBioBeta conference in San Francisco, where other presentations featured academics in suits and the young CEOs of typical biotech startups. Unlike the others, he started his workshop by handing out shots of scotch and a booklet explaining the basics of DIY [do-it-yourwelf] genome engineering.
If you want to genetically modify yourself, it turns out, it’s not necessarily complicated. As he offered samples in small baggies to the crowd, Zayner explained that it took him about five minutes to make the DNA that he brought to the presentation. The vial held Cas9, an enzyme that snips DNA at a particular location targeted by guide RNA, in the gene-editing system known as CRISPR. In this case, it was designed to knock out the myostatin gene, which produces a hormone that limits muscle growth and lets muscles atrophy. In a study in China, dogs with the edited gene had double the muscle mass of normal dogs. If anyone in the audience wanted to try it, they could take a vial home and inject it later. Even rubbing it on skin, Zayner said, would have some effect on cells, albeit limited.
Peters goes on to note that Zayner has a PhD in molecular biology and biophysics and worked for NASA (US National Aeronautics and Space Administration). Zayner’s Wikipedia entry fills in a few more details (Note: Links have been removed),
Zayner graduated from the University of Chicago with a Ph.D. in biophysics in 2013. He then spent two years as a researcher at NASA’s Ames Research Center, where he worked on Martian colony habitat design. While at the agency, Zayner also analyzed speech patterns in online chat, Twitter, and books, and found that language on Twitter and online chat is closer to how people talk than to how they write. Zayner found NASA’s scientific work less innovative than he expected, and upon leaving in January 2016, he launched a crowdfunding campaign to provide CRISPR kits to let the general public experiment with editing bacterial DNA. He also continued his grad school business, The ODIN, which sells kits to let the general public experiment at home. As of May 2016, The ODIN had four employees and operates out of Zayner’s garage.
He refers to himself as a biohacker and believes in the importance in letting the general public participate in scientific experimentation, rather than leaving it segregated to labs. Zayner found the biohacking community exclusive and hierarchical, particularly in the types of people who decide what is “safe”. He hopes that his projects can let even more people experiment in their homes. Other scientists responded that biohacking is inherently privileged, as it requires leisure time and money, and that deviance from the safety rules of concern would lead to even harsher regulations for all. Zayner’s public CRISPR kit campaign coincided with wider scrutiny over genetic modification. Zayner maintained that these fears were based on misunderstandings of the product, as genetic experiments on yeast and bacteria cannot produce a viral epidemic. In April 2015, Zayner ran a hoax on Craigslist to raise awareness about the future potential of forgery in forensics genetics testing.
In February 2016, Zayner performed a full body microbiome transplant on himself, including a fecal transplant, to experiment with microbiome engineering and see if he could cure himself from gastrointestinal and other health issues. The microbiome from the donors feces successfully transplanted in Zayner’s gut according to DNA sequencing done on samples. This experiment was documented by filmmakers Kate McLean and Mario Furloni and turned into the short documentary film Gut Hack.
In December 2016, Zayner created a fluorescent beer by engineering yeast to contain the green fluorescent protein from jellyfish. Zayner’s company, The ODIN, released kits to allow people to create their own engineered fluorescent yeast and this was met with some controversy as the FDA declared the green fluorescent protein can be seen as a color additive. Zayner, views the kit as a way that individual can use genetic engineering to create things in their everyday life.
I found the video for Zayner’s now completed crowdfunding campaign,
I also found The ODIN website (mentioned in the Wikipedia essay) where they claim to be selling various gene editing and gene engineering kits including the CRISPR editing kits mentioned in Peters’ article,
In 2016, he [Zayner] sold $200,000 worth of products, including a kit for yeast that can be used to brew glowing bioluminescent beer, a kit to discover antibiotics at home, and a full home lab that’s roughly the cost of a MacBook Pro. In 2017, he expects to double sales. Many kits are simple, and most buyers probably aren’t using the supplies to attempt to engineer themselves (many kits go to classrooms). But Zayner also hopes that as people using the kits gain genetic literacy, they experiment in wilder ways.
He questions whether traditional research methods, like randomized controlled trials, are the only way to make discoveries, pointing out that in newer personalized medicine (such as immunotherapy for cancer, which is personalized for each patient), a sample size of one person makes sense. At his workshop, he argued that people should have the choice to self-experiment if they want to; we also change our DNA when we drink alcohol or smoke cigarettes or breathe in dirty city air. Other society-sanctioned activities are more dangerous. “We sacrifice maybe a million people a year to the car gods,” he said. “If you ask someone, ‘Would you get rid of cars?’–no.” …
US researchers both conventional and DIY types such as Zayner are not the only ones who are editing genes. The Chinese study mentioned in Peters’ article was written up in an Oct. 19, 2015 article by Antonio Regalado for the MIT [Massachusetts Institute of Technology] Technology Review (Note: Links have been removed),
Scientists in China say they are the first to use gene editing to produce customized dogs. They created a beagle with double the amount of muscle mass by deleting a gene called myostatin.
The dogs have “more muscles and are expected to have stronger running ability, which is good for hunting, police (military) applications,” Liangxue Lai, a researcher with the Key Laboratory of Regenerative Biology at the Guangzhou Institutes of Biomedicine and Health, said in an e-mail.
Lai and 28 colleagues reported their results last week in the Journal of Molecular Cell Biology, saying they intend to create dogs with other DNA mutations, including ones that mimic human diseases such as Parkinson’s and muscular dystrophy. “The goal of the research is to explore an approach to the generation of new disease dog models for biomedical research,” says Lai. “Dogs are very close to humans in terms of metabolic, physiological, and anatomical characteristics.”
Lai said his group had no plans breed to breed the extra-muscular beagles as pets. Other teams, however, could move quickly to commercialize gene-altered dogs, potentially editing their DNA to change their size, enhance their intelligence, or correct genetic illnesses. A different Chinese Institute, BGI, said in September it had begun selling miniature pigs, created via gene editing, for $1,600 each as novelty pets.
People have been influencing the genetics of dogs for millennia. By at least 36,000 years ago, early humans had already started to tame wolves and shape the companions we have today. Charles Darwin frequently cited dog breeding in The Origin of Species to demonstrate how evolution gradually occurs by a process of selection. With CRISPR, however, evolution is no longer gradual or subject to chance. It is immediate and under human control.
It is precisely that power that is stirring wide debate and concern over CRISPR. Yet at least some researchers think that gene-edited dogs could put a furry, friendly face on the technology. In an interview this month, George Church, a professor at Harvard University who leads a large effort to employ CRISPR editing, said he thinks it will be possible to augment dogs by using DNA edits to make them live longer or simply make them smarter.
Church said he also believed the alteration of dogs and other large animals could open a path to eventual gene editing of people. “Germline editing of pigs or dogs offers a line into it,” he said. “People might say, ‘Hey, it works.’ ”
In the meantime, Zayner’s ideas are certainly thought provoking. I’m not endorsing either his products or his ideas but it should be noted that early science pioneers such as Humphrey Davy and others experimented on themselves. For anyone unfamiliar with Davy, (from the Humphrey Davy Wikipedia entry; Note: Links have been removed),
Sir Humphry Davy, 1st Baronet PRS MRIA FGS (17 December 1778 – 29 May 1829) was a Cornish chemist and inventor, who is best remembered today for isolating a series of substances for the first time: potassium and sodium in 1807 and calcium, strontium, barium, magnesium and boron the following year, as well as discovering the elemental nature of chlorine and iodine. He also studied the forces involved in these separations, inventing the new field of electrochemistry. Berzelius called Davy’s 1806 Bakerian Lecture On Some Chemical Agencies of Electricity “one of the best memoirs which has ever enriched the theory of chemistry.” He was a Baronet, President of the Royal Society (PRS), Member of the Royal Irish Academy (MRIA), and Fellow of the Geological Society (FGS). He also invented the Davy lamp and a very early form of incandescent light bulb.
A Nov. 11, 2017 posting on the Canadian Broadcasting Corporation’s (CBC) Quirks and Quarks blog notes that self-experimentation has a long history and goes on to describe Zayner’s and others biohacking exploits before describing the legality of biohacking in Canada,
With biohackers entering into the space traditionally held by scientists and clinicians, it begs questions. Professor Timothy Caulfield, a Canada research chair in health, law and policy at the University of Alberta, says when he hears of somebody giving themselves biohacked gene therapy, he wonders: “Is this legal? Is this safe? And if it’s not safe, is there anything that we can do about regulating it? And to be honest with you that’s a tough question and I think it’s an open question.”
In Canada, Caulfield says, Health Canada focuses on products. “You have to have something that you are going to regulate or you have to have something that’s making health claims. So if there is a product that is saying I can cure X, Y, or Z, Health Canada can say, ‘Well let’s make sure the science really backs up that claim.’ The problem with these do-it-yourself approaches is there isn’t really a product. You know these people are experimenting on themselves with something that may or may not be designed for health purposes.”
According to Caufield, if you could buy a gene therapy kit that was being marketed to you to biohack yourself, that would be different. “Health Canada could jump in. But right here that’s not the case,” he says.
There are places in the world that do regulate biohacking, says Caulfield. “Germany, for example, they have specific laws for it. And here in Canada we do have a regulatory framework that says that you cannot do gene therapy that will alter the germ line. In other words, you can’t do gene therapy or any kind of genetic editing that will create a change that you will pass on to your offspring. So that would be illegal, but that’s not what’s happening here. And I don’t think there’s a regulatory framework that adequately captures it.”
Infectious disease and policy experts aren’t that concerned yet about the possibility of a biohacker unleashing a genetically modified super germ into the population.
“I think in the future that could be a problem,”says Caulfield, “but this isn’t something that would be easy to do in your garage. I think it’s complicated science. But having said that, the science is moving quickly. We need to think about how we are going to control the potential harms.”
You can find out more about the ‘wild’ people (mostly men) of early science in Richard Holmes’ 2008 book, The Age of Wonder: How the Romantic Generation Discovered the Beauty and Terror of Science.
Finally, should you be interested in connecting with synthetic biology enthusiasts, entrepreneurs, and others, SynBioBeta is more than a conference; it’s also an activity hub.
ETA January 25, 2018 (five minutes later): There are some CRISPR/CAS9 events taking place in Toronto, Canada on January 24 and 25, 2018. One is a workshop with Portuguese artist, Marta de Menezes, and the other is a panel discussion. See my January 10, 2018 posting for more details.
*’Segue: There is some Canadian content if you keep reading.’ and ‘Canadian content’ added January 25, 2018 six minutes after first publication.
ETA February 20, 2018: Sarah Zhang’s Feb. 20, 2018 article for The Atlantic revisits Josiah Zayner’s decision to inject himself with CRISPR,
When Josiah Zayner watched a biotech CEO drop his pants at a biohacking conference and inject himself with an untested herpes treatment, he realized things had gone off the rails.
Zayner is no stranger to stunts in biohacking—loosely defined as experiments, often on the self, that take place outside of traditional lab spaces. You might say he invented their latest incarnation: He’s sterilized his body to “transplant” his entire microbiome in front of a reporter. He’s squabbled with the FDA about selling a kit to make glow-in-the-dark beer. He’s extensively documented attempts to genetically engineer the color of his skin. And most notoriously, he injected his arm with DNA encoding for CRISPR that could theoretically enhance his muscles—in between taking swigs of Scotch at a live-streamed event during an October conference. (Experts say—and even Zayner himself in the live-stream conceded—it’s unlikely to work.)
So when Zayner saw Ascendance Biomedical’s CEO injecting himself on a live-stream earlier this month, you might say there was an uneasy flicker of recognition.
“Honestly, I kind of blame myself,” Zayner told me recently. He’s been in a soul-searching mood; he recently had a kid and the backlash to the CRISPR stunt in October  had been getting to him. “There’s no doubt in my mind that somebody is going to end up hurt eventually,” he said.
Yup, it’s one of the reasons for rules; people take things too far. The trick is figuring out how to achieve balance between risk taking and recklessness.
Updates on a previous glowing plants and animals posting
In a May 5, 2013 posting I featured a Kickstarter campaign for a synthetic biology project focused on plants that emit light in the dark. I also mentioned Eduardo Kac (pronounced Katz) and his art project/transgenic bunny called Alba. At the time, I did not realize that Alba had been declared dead in 2002 adding more controversy to an already controversial topice according to Kristen Philipkoski in an Aug. 12, 2002 article (how did I miss this article in 2013?) for Wired magazine (Note: Links have been removed),
Alba, the glowing rabbit that made headlines two years ago for being, well, a glowing rabbit, has met an untimely death, according to the French researcher who genetically engineered her.
Alba the glowing rabbit was 4 years old. Or 2-1/2, depending on who’s talking.
The bunny died about a month ago for reasons that are not clear, said Louis-Marie Houdebine, a genetic researcher at France’s National Institute of Agronomic Research.
“I was informed one day that bunny was dead without any reason,” Houdebine said. “So, rabbits die often. It was about 4 years old, which is a normal lifespan in our facilities.”
Alba was an albino rabbit engineered by splicing the green fluorescent protein (GFP) of a jellyfish into her genome. Houdebine said he did not believe the GFP gene played a role in the animal’s demise.
Eduardo Kac, the artist who created a flurry by making her a work of art, doesn’t buy it, however.
First, Alba’s not 4, she’s 2-1/2, Kac says (a rabbit’s lifespan is up to 12 years), because she was bred by Houdebine specifically for him in January 2000.
Houdebine says he simply picked a rabbit with a gentle disposition that was already in his lab.
Second, he believes Houdebine might be declaring the bunny gone in order to put an end to a two-year, unwelcome barrage of media attention.
If she really is dead, Kac will never realize the final phase of his project, which was to take Alba home and keep her as a pet.
Kac says he and Houdebine originally collaborated on the GFP bunny project, until Houdebine’s director put the kibosh on it.
“My director did not understand,” Houdebine said. “He said I should not give the rabbit (to someone) outside the lab.”
Houdebine said that yes, they spoke about preliminary plans for Kac to use the bunny for his project and take it to an art show in Avignon. But he denies he bred an animal specifically for Kac.
Houdebine says he would not have agreed to engineer one animal specifically for any artist.
This disputed point has led fellow artists and critics to question whether Kac can rightly take credit for the Alba project.
But Kac insists that Houdebine did, in fact, agree to make the bunny specifically for him.
Kac found out sometime in mid-2000 that Houdebine’s director had a problem with the project and would not allow the rabbit to be taken from the lab.
Houdebine was initially apologetic, Kac said. But after an article ran on the front page of the Boston Globe on Sept. 17, 2000, their relationship cooled.
Houdebine and his director were opposed to the now-famous, brilliantly glowing photograph of Alba. They and other researchers say the rabbit doesn’t actually glow so brightly and uniformly.
“Kac fabricated data for his personal use,” Houdebine said. “This is why we totally stopped any contact with him.”
“The scientific fact is that the rabbit is not green,” he said. “He should have never published that. This was very disagreeable for me.”
Kac believes the scientists were simply afraid of public criticism. Meanwhile, he wanted to do the opposite – to encourage discourse on the transgenic rabbit.
“This director refuses to participate openly in a debate about what is done with public money,” he said. “It’s very easy to fear and reject what you don’t know. As long as they continue to isolate themselves, this mistrust will continue.”
The eyes and ears of the rabbit are green under ultraviolet light, Houdebine said, but the fur does not glow, because it’s dead tissue that doesn’t express the gene. Only if the rabbit were shaved would the body glow, he said.
Philipkosk’s article provides some insight into the interface between art and science and is worth reading in its entirety if you have the time.
I’ve also found an update for the glowing plants Kickstarter campaign in an April 20, 2017 article by Sarah Zhang for The Atlantic (Note: Links have been removed),
The latest update came quietly on Tuesday night [April 18, 2017?]. “We’re sorry to say that we have reached a significant transition point,” wrote the Glowing Plant project’s creator, Antony Evans. This “transition point” was more of an endpoint: The project had run out of money. The quest to genetically engineer a glow-in-the-dark plant was no more.
Four years ago, the Glowing Plant project raised nearly half a million dollars on Kickstarter, easily blowing past its initial ask of $65,000. Of course it did. The vision it presented was such potent fantasy. “What if,” Evans asked over swelling music in the pitch video, “we use trees to light our streets instead of street lamps?” What if you could get lighting without electricity? What if the natural world glowed like in Avatar?
This romantic vision so perfectly encapsulated the promises of synthetic biology, a field that treats the natural world as another system to be designed and engineered. In this case, synthetic biology became a possible solution to one of the world’s most pressing energy problems: electricity generation. Plus, it sounded really damn cool.
The Kickstarter campaign only promised a small, potted glowing plant to it backers, and I doubt many backers actually harbored illusions about trees lighting up the night sky soon. But backing the project was a small way to buy into a much grander vision.
At a time when “genetically modified organism,” or GMO, is such a poisoned phrase, the project’s crowdfunding success seemed to suggest that a pervasive if vague distrust of genetic modification might be countered by the sense of wonder for a glowing plant. (As the Kickstarter campaign grew, though, environmental groups raised questions and the crowdfunding site later banned giving away genetically modified organisms.)
The team also encountered the hard realities of engineering even a small plant that glows. “We did not anticipate some of the unknown technical challenges that we would get into,” Evans told me. (Plenty of scientists at the time were skeptical of the project’s timeline, though.) Evans is an MBA with a background in mobile apps, though his two original cofounders, who have both since left the project, had backgrounds in synthetic biology.
To get the plant to glow well, the research team had to insert six genes. But they never could get all six in at once. At best, some plants glowed very dimly. (The photo above of the glowing plant is a long exposure, making it appear much brighter than it actually is.) Evans says that he realizes now trying to insert six genes into a complex organism like a plant—rather than single-celled bacteria or yeast—was premature.
“I’m really afraid of disappointing that 16-year-old who saw this and imagined a bright wonderful future, of jading and disappointing people,” he says. Despite a few angry backers asking for a refund, most of the comments under the Kickstarter update so far have been supportive. The project had been providing regular, detailed updates on the difficulty of engineering the plants. The latest update was its 67th.
Zhang’s article goes on to detail other synthetic biology projects, which are showing some promise.
When you take this work into consideration with CRISPR-CAS9 and the beginnings of genetic germline editing, the question has to be asked: Will public discussion (if there’s any) be considered upstream (early in the process) or downstream (after the work has been done)? Public engagement professionals tend to favour upstream discussions, i.e., before people start demanding fear-based policy.