Trying to get a handle on CRISPR news in 2019 can be daunting if you haven't been avidly reading up on it for the last five years.
CRISPR as a diagnostic tool would be a major game changer for medicine and agriculture.
On top of trying to grasp how the science works, and keeping track of its ever expanding applications, you may also have seen coverage of an ongoing legal battle about who owns the intellectual property behind the gene-editing technology CRISPR-Cas9. And then there's the infamous controversy surrounding a scientist who claimed to have used the tool to edit the genomes of two babies in China last year.
But gene editing is not the only application of CRISPR-based biotechnologies. In the future, it may also be used as a tool to diagnose infectious diseases, which could be a major game changer for medicine and agriculture.
How It Works
CRISPR is an acronym for a naturally occurring DNA sequence that normally protects microbes from viruses. It's been compared to a Swiss army knife that can recognize an invader's DNA and precisely destroy it. Repurposed for humans, CRISPR can be paired with a protein called Cas9 that can detect a person's own DNA sequence (usually a problematic one), cut it out, and replace it with a different sequence. Used this way, CRISPR-Cas9 has become a valuable gene-editing tool that is currently being tested to treat numerous genetic diseases, from cancer to blood disorders to blindness.
CRISPR can also be paired with other proteins, like Cas13, which target RNA, the single-stranded twin of DNA that viruses rely on to infect their hosts and cause disease. In a future clinical setting, CRISPR-Cas13 might be used to diagnose whether you have the flu by cutting a target RNA sequence from the virus. That spliced sequence could stick to a paper test strip, causing a band to show up, like on a pregnancy test strip. If the influenza virus and its RNA are not present, no band would show up.
To understand how close to reality this diagnostic scenario is right now, leapsmag chatted with CRISPR pioneer Dr. Feng Zhang, a molecular biologist at the Broad Institute of MIT and Harvard.
What do you think might be the first point of contact that a regular person or patient would have with a CRISPR diagnostic tool?
FZ: I think in the long run it will be great to see this for, say, at-home disease testing, for influenza and other sorts of important public health [concerns]. To be able to get a readout at home, people can potentially quarantine themselves rather than traveling to a hospital and then carrying the risk of spreading that disease to other people as they get to the clinic.
"You could conceivably get a readout during the same office visit, and then the doctor will be able to prescribe the right treatment right away."
Is this just something that people will use at home, or do you also foresee clinical labs at hospitals applying CRISPR-Cas13 to samples that come through?
FZ: I think we'll see applications in both settings, and I think there are advantages to both. One of the nice things about SHERLOCK [a playful acronym for CRISPR-Cas13's longer name, Specific High-sensitivity Enzymatic Reporter unLOCKing] is that it's rapid; you can get a readout fairly quickly. So, right now, what people do in hospitals is they will collect your sample and then they'll send it out to a clinical testing lab, so you wouldn't get a result back until many hours if not several days later. With SHERLOCK, you could conceivably get a readout during the same office visit, and then the doctor will be able to prescribe the right treatment right away.
I just want to clarify that when you say a doctor would take a sample, that's referring to urine, blood, or saliva, correct?
FZ: Right. Yeah, exactly.
Thinking more long term, are there any Holy Grail applications that you hope CRISPR reaches as a diagnostic tool?
FZ: I think in the developed world we'll hopefully see this being used for influenza testing, and many other viral and pathogen-based diseases—both at home and also in the hospital—but I think the even more exciting direction is that this could be used and deployed in parts of the developing world where there isn't a fancy laboratory with elaborate instrumentation. SHERLOCK is relatively inexpensive to develop, and you can turn it into a paper strip test.
Can you quantify what you mean by relatively inexpensive? What range of prices are we talking about here?
FZ: So without accounting for economies of scale, we estimate that it can cost less than a dollar per test. With economy of scale that cost can go even lower.
Is there value in developing what is actually quite an innovative tool in a way that visually doesn't seem innovative because it's reminiscent of a pregnancy test? And I don't mean that as an insult.
FZ: [Laughs] Ultimately, we want the technology to be as accessible as possible, and pregnancy test strips have such a convenient and easy-to-use form. I think modeling after something that people are already familiar with and just changing what's under the hood makes a lot of sense.
(Photo credit: Justin Knight, McGovern Institute)
It's probably one of the most accessible at-home diagnostic tools at this point that people are familiar with.
FZ: Yeah, so if people know how to use that, then using something that's very similar to it should make the option very easy.
You've been quite vocal in calling for some pauses in CRISPR-Cas9 research to make sure it doesn't outpace the ethics of establishing pregnancies with that version of the tool. Do you have any concerns about using CRISPR-Cas13 as a diagnostic tool?
I think overall, the reception for CRISPR-based diagnostics has been overwhelmingly positive. People are very excited about the prospect of using this—for human health and also in agriculture [for] detection of plant infections and plant pathogens, so that farmers will be able to react quickly to infection in the field. If we're looking at contamination of foods by certain bacteria, [food safety] would also be a really exciting application.
Do you feel like the controversies surrounding using CRISPR as a gene-editing tool have overshadowed its potential as a diagnostics tool?
FZ: I don't think so. I think the potential for using CRISPR-Cas9 or CRISPR-Cas12 for gene therapy, and treating disease, has captured people's imaginations, but at the same time, every time I talk with someone about the ability to use CRISPR-Cas13 as a diagnostic tool, people are equally excited. Especially when people see the very simple paper strip that we developed for detecting diseases.
Are CRISPR as a gene-editing tool and CRISPR as a diagnostics tool on different timelines, as far as when the general public might encounter them in their real lives?
FZ: I think they are all moving forward quite quickly. CRISPR as a gene-editing tool is already being deployed in human health and agriculture. We've already seen the approval for the development of growing genome-edited mushrooms, soybeans, and other crop species. So I think people will encounter those in their daily lives in that manner.
Then, of course, for disease treatment, that's progressing rapidly as well. For patients who are affected by sickle cell disease, and also by a degenerative eye disease, clinical trials are already starting in those two areas. Diagnostic tests are also developing quickly, and I think in the coming couple of years, we'll begin to see some of these reaching into the public realm.
"There are probably 7,000 genetic diseases identified today, and most of them don't have any way of being treated."
As far its limits, will it be hard to use CRISPR as a diagnostic tool in situations where we don't necessarily understand the biological underpinnings of a disease?
FZ: CRISPR-Cas13, as a diagnostic tool, at least in the current way that it's implemented, is a detection tool—it's not a discovery tool. So if we don't know what we're looking for, then it's going to be hard to develop Cas13 to detect it. But even in the case of a new infectious disease, if DNA sequencing or RNA sequencing information is available for that new virus, then we can very rapidly program a Cas13-based system to detect it, based on that sequence.
What's something you think the public misunderstands about CRISPR, either in general, or specifically as a diagnostic tool, that you wish were better understood?
FZ: That's a good question. CRISPR-Cas9 and CRISPR-Cas12 as gene editing tools, and also CRISPR-Cas13 as a diagnostic tool, are able to do some things, but there are still a lot of capabilities that need to be further developed. So I think the potential for the technology will unfold over the next decade or so, but it will take some time for the full impact of the technology to really get realized in real life.
What do you think that full impact is?
FZ: There are probably 7,000 genetic diseases identified today, and most of them don't have any way of being treated. It will take some time for CRISPR-Cas9 and Cas12 to be really developed for addressing a larger number of those diseases. And then for CRISPR-based diagnostics, I think you'll see the technology being applied in a couple of initial cases, and it will take some time to develop that more broadly for many other applications.
A natural material that looks and feels like real leather is taking the fashion world by storm. Scientists view mycelium—the vegetative part of a mushroom-producing fungus—as a planet-friendly alternative to animal hides and plastics.
Products crafted from this vegan leather are emerging, with others poised to hit the market soon. Among them are the Hermès Victoria bag, Lululemon's yoga accessories, Adidas' Stan Smith Mylo sneaker, and a Stella McCartney apparel collection.
The Adidas Stan Smith Mylo shoe, made with an alternative leather grown from mycelium, to be released in 2022.
Hermès has held presales on the new bag, says Philip Ross, co-founder and chief technology officer of MycoWorks, a San Francisco Bay area firm whose materials constituted the design. By year-end, Ross expects several more clients to debut mycelium-based merchandise. With "comparable qualities to luxury leather," mycelium can be molded to engineer "all the different verticals within fashion," he says, particularly footwear and accessories.
More than a half-dozen trailblazers are fine-tuning mycelium to create next-generation leather materials, according to the Material Innovation Initiative, a nonprofit advocating for animal-free materials in the fashion, automotive, and home-goods industries. These high-performance products can supersede items derived from leather, silk, down, fur, wool, and exotic skins, says A. Sydney Gladman, the institute's chief scientific officer.
That's only the beginning of mycelium's untapped prowess. "We expect to see an uptick in commercial leather alternative applications for mycelium-based materials as companies refine their R&D [research and development] and scale up," Gladman says, adding that "technological innovation and untapped natural materials have the potential to transform the materials industry and solve the enormous environmental challenges it faces."
In fewer than 10 days in indoor agricultural farms, "we grow large slabs of mycelium that are many feet wide and long. We are not confined to the shape or geometry of an animal."
Reducing our carbon footprint becomes possible because mycelium can flourish in indoor farms, using agricultural waste as feedstock and emitting inherently low greenhouse gas emissions. Carbon dioxide is the primary greenhouse gas. "We often think that when plant tissues like wood rot, that they go from something to nothing," says Jonathan Schilling, professor of plant and microbial biology at the University of Minnesota and a member of MycoWorks' Scientific Advisory Board.
But that assumption doesn't hold true for all carbon in plant tissues. When the fungi dominating the decomposition of plants fulfill their function, they transform a large portion of carbon into fungal biomass, Schilling says. That, in turn, ends up in the soil, with mycelium forming a network underneath that traps the carbon.
Unlike the large amounts of fossil fuels needed to produce styrofoam, leather and plastic, less fuel-intensive processing is involved in creating similar materials with a fungal organism. While some fungi consist of a single cell, others are multicellular and develop as very fine threadlike structures. A mass of them collectively forms a "mycelium" that can be either loose and low density or tightly packed and high density. "When these fungi grow at extremely high density," Schilling explains, "they can take on the feel of a solid material such as styrofoam, leather or even plastic."
Tunable and supple in the cultivation process, mycelium is also reliably sturdy in composition. "We believe that mycelium has some unique attributes that differentiate it from plastic-based and animal-derived products," says Gavin McIntyre, who co-founded Ecovative Design, an upstate New York-based biomaterials company, in 2007 with the goal of displacing some environmentally burdensome materials and making "a meaningful impact on our planet."
After inventing a type of mushroom-based packaging for all sorts of goods, in 2013 the firm ventured into manufacturing mycelium that can be adapted for textiles, he says, because mushrooms are "nature's recycling system."
The company aims for its material—which is "so tough and tenacious" that it doesn't require any plastic add-on as reinforcement—to be generally accessible from a pricing standpoint and not confined to a luxury space. The cost, McIntyre says, would approach that of bovine leather, not the more upscale varieties of lamb and goat skins.
Already, production has taken off by leaps and bounds. In fewer than 10 days in indoor agricultural farms, "we grow large slabs of mycelium that are many feet wide and long," he says. "We are not confined to the shape or geometry of an animal," so there's a much lower scrap rate.
Decreasing the scrap rate is a major selling point. "Our customers can order the pieces to the way that they want them, and there is almost no waste in the processing," explains Ross of MycoWorks. "We can make ours thinner or thicker," depending on a client's specific needs. Growing materials locally also results in a reduction in transportation, shipping and other supply chain costs, he says.
Yet another advantage to making things out of mycelium is its biodegradability at the end of an item's lifecycle. When a pair of old sneakers lands in a compost pile or landfill, it decomposes thanks to microbial processes that, once again, involve fungi. "It is cool to think that the same organism used to create a product can also be what recycles it, perhaps building something else useful in the same act," says biologist Schilling. That amounts to "more than a nice business model—it is a window into how sustainability works in nature."
A product can be called "sustainable" if it's biodegradable, leaves a minimal carbon footprint during production, and is also profitable, says Preeti Arya, an assistant professor at the Fashion Institute of Technology in New York City and faculty adviser to a student club of the American Association of Textile Chemists and Colorists.
On the opposite end of the spectrum, products composed of petroleum-based polymers don't biodegrade—they break down into smaller pieces or even particles. These remnants pollute landfills, oceans and rivers, contaminating edible fish and eventually contributing to the growth of benign and cancerous tumors in humans, Arya says.
Commending the steps a few designers have taken toward bringing more environmentally conscious merchandise to consumers, she says, "I'm glad that they took the initiative because others also will try to be part of this competition toward sustainability." And consumers will take notice. "The more people become aware, the more these brands will start acting on it."
A further shift toward mycelium-based products has the capability to reap tremendous environmental dividends, says Drew Endy, associate chair of bioengineering at Stanford University and president of the BioBricks Foundation, which focuses on biotechnology in the public interest.
The continued development of "leather surrogates on a scaled and sustainable basis will provide the greatest benefit to the greatest number of people, in perpetuity," Endy says. "Transitioning the production of leather goods from a process that involves the industrial-scale slaughter of vertebrate mammals to a process that instead uses renewable fungal-based manufacturing will be more just."
Amy Bitterman, who teaches at Rutgers Law School in Newark, gets enormous pleasure from her three mixed-breed rescue cats, Spike, Dee, and Lucy. To manage her chronically stuffy nose, three times a week she takes Allegra D, which combines the antihistamine fexofenadine with the decongestant pseudoephedrine. Amy's dog allergy is rougher--so severe that when her sister launched a business, Pet Care By Susan, from their home in Edison, New Jersey, they knew Susan would have to move elsewhere before she could board dogs. Amy has tried to visit their brother, who owns a Labrador Retriever, taking Allegra D beforehand. But she began sneezing, and then developed watery eyes and phlegm in her chest.
"It gets harder and harder to breathe," she says.
Animal lovers have long dreamed of "hypo-allergenic" cats and dogs. Although to date, there is no such thing, biotechnology is beginning to provide solutions for cat-lovers. Cats are a simpler challenge than dogs. Dog allergies involve as many as seven proteins. But up to 95 percent of people who have cat allergies--estimated at 10 to 30 percent of the population in North America and Europe--react to one protein, Fel d1. Interestingly, cats don't seem to need Fel d1. There are cats who don't produce much Fel d1 and have no known health problems.
The current technologies fight Fel d1 in ingenious ways. Nestle Purina reached the market first with a cat food, Pro Plan LiveClear, launched in the U.S. a year and a half ago. It contains Fel d1 antibodies from eggs that in effect neutralize the protein. HypoCat, a vaccine for cats, induces them to create neutralizing antibodies to their own Fel d1. It may be available in the United States by 2024, says Gary Jennings, chief executive officer of Saiba Animal Health, a University of Zurich spin-off. Another approach, using the gene-editing tool CRISPR to create a medication that would splice out Fel d1 genes in particular tissues, is the furthest from fruition.
"Our goal was to ensure that whatever we do has no negative impact on the cat."
Customer demand is high. "We already have a steady stream of allergic cat owners contacting us desperate to have access to the vaccine or participate in the testing program," Jennings said. "There is a major unmet medical need."
More than a third of Americans own a cat (while half own a dog), and pet ownership is rising. With more Americans living alone, pets may be just the right amount of company. But the number of Americans with asthma increases every year. Of that group, some 20 to 30 percent have pet allergies that could trigger a possibly deadly attack. It is not clear how many pets end up in shelters because their owners could no longer manage allergies. Instead, allergists commonly report that their patients won't give up a beloved companion.
No one can completely avoid Fel d1, which clings to clothing and lands everywhere cat-owners go, even in schools and new homes never occupied by cats. Myths among cat-lovers may lead them to underestimate their own level of risk. Short hair doesn't help: the length of cat hair doesn't affect the production of Fel d1. Bathing your cat will likely upset it and accomplish little. Washing cuts the amount on its skin and fur only for two days. In one study, researchers measured the Fel d1 in the ambient air in a small chamber occupied by a cat—and then washed the cat. Three hours later, with the cat in the chamber again, the measurable Fel d1 in the air was lower. But this benefit was gone after 24 hours.
For years, the best option has been shots for people that prompt protective antibodies. Bitterman received dog and cat allergy injections twice a week as a child. However, these treatments require up to 100 injections over three to five years, and, as in her case, the effect may be partial or wear off. Even if you do opt for shots, treating the cat also makes sense, since you could protect more than one allergic member of your household and any allergic visitors as well.
An Allergy-Neutralizing Diet
Cats produce much of their Fel d1 in their saliva, which then spreads it to their fur when they groom, observed Nestle Purina immunologist Ebenezer Satyaraj. He realized that this made saliva—and therefore a cat's mouth--an unusually effective site for change. Hens exposed to Fel d1 produce their own antibodies, which survive in their eggs. The team coated LiveClear food with a powder form of these eggs; once in a cat's mouth, the chicken antibody binds to the Fel d1 in the cat's saliva, neutralizing it.
The results are partial: In a study with 105 cats, the level of active Fel d1 in their fur had dropped on average by 47 percent after ten weeks eating LiveClear. Cats that produced more Fel d1 at baseline had a more robust response, with a drop of up to 71 percent. A safety study found no effects on cats after six months on the diet. "Our goal was to ensure that whatever we do has no negative impact on the cat," Satyaraj said. Might a dogfood that minimizes dog allergens be on the way? "There is some early work," he said.
This is a year when vaccines changed the lives of billions. Saiba's vaccine, HypoCat, delivers recombinant Fel d1 and the coat from a plant virus (the Cucumber mosaic virus) without any vital genetic information. The viral coat serves as a carrier. A cat would need shots once or twice a year to produce antibodies that neutralize Fel d1.
HypoCat works much like any vaccine, with the twist that the enemy is the cat's own protein. Is that safe? Saiba's team has followed 70 cats treated with the vaccine over two years and they remain healthy. Again the active Fel d1 doesn't disappear but diminishes. The team asked 10 people with cat allergies to report on their symptoms when they pet their vaccinated cats. Eight of them could pet their cat for nearly a half hour before their symptoms began, compared with an average of 17 minutes before the vaccine.
Jennings hopes to develop a HypoDog shot with a similar approach. However, the goal would be to target four or five proteins in one vaccine, and that increases the risk of hurting the dog. In the meantime, allergic dog-lovers considering an expensive breeder dog might think again: Independent research does not support the idea that any breed of dog produces less dander in the home. In fact, one well-designed study found that Spanish water dogs, Airedales, poodles and Labradoodles--breeds touted as hypo-allergenic--had significantly more of the most common allergen on their coat than an ordinary Lab and the control group.
One day you might be able to bring your cat to the vet once a year for an injection that would modify specific tissues so they wouldn't produce Fel d1.
Nicole Brackett, a postdoctoral scientist at Viriginia-based Indoor Biotechnologies, which specializes in manufacturing biologics for allergy and asthma, most recently has used CRISPR to identify Fel d1 genetic sequences in cells from 50 domestic cats and 24 exotic ones. She learned that the sequences vary substantially from one cat to the next. This discovery, she says, backs up the observations that Fel d1 doesn't have a vital purpose.
The next step will be a CRISPR knockout of the relevant genes in cells from feline salivary glands, a prime source of Fel d1. Although the company is considering using CRISPR to edit the genes in a cat embryo and possibly produce a Fel d1-free cat, designer cats won't be its ultimate product. Instead, the company aims to produce injections that could treat any cat.
Reducing pet allergens at home could have a compound benefit, Indoor Biotechnologies founder Martin Chapman, an immunologist, notes: "When you dampen down the response to one allergen, you could also dampen it down to multiple allergens." As allergies become more common around the world, that's especially good news.