Testing for Any Infectious Disease Could Soon Be As Simple As Peeing On a Stick
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.
Feng Zhang
(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.
This man spent over 70 years in an iron lung. What he was able to accomplish is amazing.
It’s a sight we don’t normally see these days: A man lying prone in a big, metal tube with his head sticking out of one end. But it wasn’t so long ago that this sight was unfortunately much more common.
In the first half of the 20th century, tens of thousands of people each year were infected by polio—a highly contagious virus that attacks nerves in the spinal cord and brainstem. Many people survived polio, but a small percentage of people who did were left permanently paralyzed from the virus, requiring support to help them breathe. This support, known as an “iron lung,” manually pulled oxygen in and out of a person’s lungs by changing the pressure inside the machine.
Paul Alexander was one of several thousand who were infected and paralyzed by polio in 1952. That year, a polio epidemic swept the United States, forcing businesses to close and polio wards in hospitals all over the country to fill up with sick children. When Paul caught polio in the summer of 1952, doctors urged his parents to let him rest and recover at home, since the hospital in his home suburb of Dallas, Texas was already overrun with polio patients.
Paul rested in bed for a few days with aching limbs and a fever. But his condition quickly got worse. Within a week, Paul could no longer speak or swallow, and his parents rushed him to the local hospital where the doctors performed an emergency procedure to help him breathe. Paul woke from the surgery three days later, and found himself unable to move and lying inside an iron lung in the polio ward, surrounded by rows of other paralyzed children.
Hospitals were commonly filled with polio patients who had been paralyzed by the virus before a vaccine became widely available in 1955. Associated Press
Paul struggled inside the polio ward for the next 18 months, bored and restless and needing to hold his breath when the nurses opened the iron lung to help him bathe. The doctors on the ward frequently told his parents that Paul was going to die.But against all odds, Paul lived. And with help from a physical therapist, Paul was able to thrive—sometimes for small periods outside the iron lung.
The way Paul did this was to practice glossopharyngeal breathing (or as Paul called it, “frog breathing”), where he would trap air in his mouth and force it down his throat and into his lungs by flattening his tongue. This breathing technique, taught to him by his physical therapist, would allow Paul to leave the iron lung for increasing periods of time.
With help from his iron lung (and for small periods of time without it), Paul managed to live a full, happy, and sometimes record-breaking life. At 21, Paul became the first person in Dallas, Texas to graduate high school without attending class in person, owing his success to memorization rather than taking notes. After high school, Paul received a scholarship to Southern Methodist University and pursued his dream of becoming a trial lawyer and successfully represented clients in court.
Paul Alexander, pictured here in his early 20s, mastered a type of breathing technique that allowed him to spend short amounts of time outside his iron lung. Paul Alexander
Paul practiced law in North Texas for more than 30 years, using a modified wheelchair that held his body upright. During his career, Paul even represented members of the biker gang Hells Angels—and became so close with them he was named an honorary member.Throughout his long life, Paul was also able to fly on a plane, visit the beach, adopt a dog, fall in love, and write a memoir using a plastic stick to tap out a draft on a keyboard. In recent years, Paul joined TikTok and became a viral sensation with more than 330,000 followers. In one of his first videos, Paul advocated for vaccination and warned against another polio epidemic.
Paul was reportedly hospitalized with COVID-19 at the end of February and died on March 11th, 2024. He currently holds the Guiness World Record for longest survival inside an iron lung—71 years.
Polio thankfully no longer circulates in the United States, or in most of the world, thanks to vaccines. But Paul continues to serve as a reminder of the importance of vaccination—and the power of the human spirit.
““I’ve got some big dreams. I’m not going to accept from anybody their limitations,” he said in a 2022 interview with CNN. “My life is incredible.”
When doctors couldn’t stop her daughter’s seizures, this mom earned a PhD and found a treatment herself.
Twenty-eight years ago, Tracy Dixon-Salazaar woke to the sound of her daughter, two-year-old Savannah, in the midst of a medical emergency.
“I entered [Savannah’s room] to see her tiny little body jerking about violently in her bed,” Tracy said in an interview. “I thought she was choking.” When she and her husband frantically called 911, the paramedic told them it was likely that Savannah had had a seizure—a term neither Tracy nor her husband had ever heard before.
Over the next several years, Savannah’s seizures continued and worsened. By age five Savannah was having seizures dozens of times each day, and her parents noticed significant developmental delays. Savannah was unable to use the restroom and functioned more like a toddler than a five-year-old.
Doctors were mystified: Tracy and her husband had no family history of seizures, and there was no event—such as an injury or infection—that could have caused them. Doctors were also confused as to why Savannah’s seizures were happening so frequently despite trying different seizure medications.
Doctors eventually diagnosed Savannah with Lennox-Gaustaut Syndrome, or LGS, an epilepsy disorder with no cure and a poor prognosis. People with LGS are often resistant to several kinds of anti-seizure medications, and often suffer from developmental delays and behavioral problems. People with LGS also have a higher chance of injury as well as a higher chance of sudden unexpected death (SUDEP) due to the frequent seizures. In about 70 percent of cases, LGS has an identifiable cause such as a brain injury or genetic syndrome. In about 30 percent of cases, however, the cause is unknown.
Watching her daughter struggle through repeated seizures was devastating to Tracy and the rest of the family.
“This disease, it comes into your life. It’s uninvited. It’s unannounced and it takes over every aspect of your daily life,” said Tracy in an interview with Today.com. “Plus it’s attacking the thing that is most precious to you—your kid.”
Desperate to find some answers, Tracy began combing the medical literature for information about epilepsy and LGS. She enrolled in college courses to better understand the papers she was reading.
“Ironically, I thought I needed to go to college to take English classes to understand these papers—but soon learned it wasn’t English classes I needed, It was science,” Tracy said. When she took her first college science course, Tracy says, she “fell in love with the subject.”
Tracy was now a caregiver to Savannah, who continued to have hundreds of seizures a month, as well as a full-time student, studying late into the night and while her kids were at school, using classwork as “an outlet for the pain.”
“I couldn’t help my daughter,” Tracy said. “Studying was something I could do.”
Twelve years later, Tracy had earned a PhD in neurobiology.
After her post-doctoral training, Tracy started working at a lab that explored the genetics of epilepsy. Savannah’s doctors hadn’t found a genetic cause for her seizures, so Tracy decided to sequence her genome again to check for other abnormalities—and what she found was life-changing.
Tracy discovered that Savannah had a calcium channel mutation, meaning that too much calcium was passing through Savannah’s neural pathways, leading to seizures. The information made sense to Tracy: Anti-seizure medications often leech calcium from a person’s bones. When doctors had prescribed Savannah calcium supplements in the past to counteract these effects, her seizures had gotten worse every time she took the medication. Tracy took her discovery to Savannah’s doctor, who agreed to prescribe her a calcium blocker.
The change in Savannah was almost immediate.
Within two weeks, Savannah’s seizures had decreased by 95 percent. Once on a daily seven-drug regimen, she was soon weaned to just four, and then three. Amazingly, Tracy started to notice changes in Savannah’s personality and development, too.
“She just exploded in her personality and her talking and her walking and her potty training and oh my gosh she is just so sassy,” Tracy said in an interview.
Since starting the calcium blocker eleven years ago, Savannah has continued to make enormous strides. Though still unable to read or write, Savannah enjoys puzzles and social media. She’s “obsessed” with boys, says Tracy. And while Tracy suspects she’ll never be able to live independently, she and her daughter can now share more “normal” moments—something she never anticipated at the start of Savannah’s journey with LGS. While preparing for an event, Savannah helped Tracy get ready.
“We picked out a dress and it was the first time in our lives that we did something normal as a mother and a daughter,” she said. “It was pretty cool.”