Lake Wright was born in Winchester, England, on March 4, 1999. At five and a half pounds, he seemed perfect, in the way newborn babies do. A week later, though, his mother, Rachel Wright, got news about her son that she’d hoped never to hear. There was something broken inside each of Lake’s cells. It was just a tiny mistake in the DNA sequence along his X chromosome, but it would lead to a major problem. Neutrophils in his bloodstream — essential components in the body’s first line of defense against infectious bacteria and fungi — wouldn’t be up to the task of protecting Lake’s tissues. The rare immune disorder, called chronic granulomatous disease (CGD), would mean a steady diet of antibiotic and anti-fungal medications, countless CT scans, and frequent, sometimes prolonged hospital stays to manage life-threatening infections.
The news came as a shock, if not a surprise. That’s because, as Rachel tells it, Lake’s story began back in 1982, when his uncle’s persistent struggle with infections as a young person led to his diagnosis with X-linked CGD. The diagnosis prompted testing of other family members for the presence of the CGD mutation. Rachel’s one good X chromosome would keep her immune system in working order, but she was a carrier, as was her mom.
Having witnessed what her brother went through growing up as a CGD sufferer, Rachel knew all too well what Lake’s diagnosis really meant. Even with aggressive anti-microbial treatments, patients with CGD are strongly advised to make lifestyle changes, says Suk See De Ravin from the National Institute of Allergy and Infectious Diseases (NIAID) in Bethesda, Maryland. “They must avoid situations where there would be increased risk of infection,” she says. “Playing in the dirt, raking up leaves … these are all no-no activities.”
The reason those activities are no-nos for kids or adults with CGD is because of the molds and mold spores that lurk in many places, both indoors and out. Most of us can and do breathe those spores into our lungs daily without issue. But in people with compromised immune systems, the risk of developing a life-threatening fungal infection is simply too great. Despite precautions, when Lake was 2 years old, he fell sick with his first serious infection, as Aspergillus mold took up residence in his left lung. He was treated in the hospital and recovered, but a chronic case of colitis (inflammation of the colon) soon followed.
He spent the next eight years in treatment to keep the infections and inflammation in check and then, his mother says, “the unthinkable happened.” His infection turned into severe and life-threatening sepsis. There were complications, including fluid on his brain, prompting his doctors to put him into a medically induced coma for more than three weeks.
“One of the doctors had already warned me that Lake may not be able to breathe, eat, or walk for himself again,” Rachel wrote on a Facebook page called Lake v. CGD, dedicated to chronicling her son’s condition. “I struggled to cope with the news and locked myself in my car until it fully sank in.”
The Lowdown on CRISPR’s Bitter Patent Dispute
For more than a year, researchers credited with demonstrating the first uses of CRISPR-Cas9 for gene editing have been locked in what experts describe as an unusually bitter patent dispute. At issue is whether patents awarded to Feng Zhang of the Broad Institute in 2014 interfere with patent applications filed earlier by Jennifer Doudna at the University of California, Berkeley, and Emmanuelle Charpentier, now at the Max Planck Institute for Infection Biology in Berlin and Umeå University in Sweden. All three are involved in companies looking to apply CRISPR to disease treatment.Doudna and Charpentier were the first to show that CRISPR works as a DNA editor in a test tube. The labs of George Church (of Harvard University) and Zhang were the first to each, independently, publish evidence that CRISPR also works in mammalian cells. Questions about the intellectual property rights for the CRISPR technology hinged in part on whether the elements those patents cover should be considered essentially the same or not. In February 2017, a ruling by the U.S. Patent Trial and Appeal Board sided with the Broad Institute. In April Berkeley appealed the decision.The good news for all those awaiting progress in bringing CRISPR to the clinic is that, so far, the arguments in the courtroom don’t seem to have impeded progress on CRISPR-based treatments. CRISPR technology is widely available for research use. It’s less clear what will happen when CRISPR-based therapies become commercially available. Stay tuned.
Forty-six-year-old Robert Karp doesn’t know Lake, but his early life followed a remarkably similar story line. Karp and his older brother were born in South Africa; both have CGD. He and his family later moved to the U.S., where they found a pediatrician who was well informed on the rare immune deficiency at the University of Tennessee. But the younger Karp still landed in the hospital with his first major infectious episode at the age of 11. His doctor got him to experts at the NIAID in Bethesda, where research on CGD was underway. Karp had a massive Aspergillus infection in his spine and lower brain. He spent four months in the hospital, receiving hefty doses of IV antibiotics and transfusions to restore his white blood cells.
In those days, CGD research was focused on learning how to manage the disease, using aggressive anti-microbial treatments to combat the inevitable infections and, in some cases, invasive surgeries to remove infected masses of tissue. Karp’s family and more than 200 other CGD-affected families have been a part of that research for many years. He says, rather nonchalantly, that he participated in an earlier trial of gene therapy, in which his cells were treated with a virus carrying the working gene he’s missing, but the experimental treatment in his case didn’t pan out. Now, Karp says, after all these years, and more surgeries than he can count, he and his brother think for the first time that they might be seeing real hope for themselves and for kids like Lake.
The light that Karp now sees is all because of a gene-editing tool called CRISPR-Cas9. The CRISPR tool includes a cutting enzyme, often likened to a pair of scissors, which researchers have borrowed from bacteria. A key feature of these molecular scissors is that they can be readily programmed to cut the genome very precisely with the addition of short snippets of guide RNA that match the gene (or genes) of interest. In some cases, cutting out a gene might be all that’s needed to get the desired effect. In others, researchers can insert a template including the desired gene sequence, directing the cell to swap out the broken gene a person was born with for a healthy one. While there are other gene-editing tools with a longer history, CRISPR’s ease and precision have quickly led to what many consider a biological revolution.
In a recent report in Science Translational Medicine, De Ravin and her colleagues, including Harry Malech, who has studied CGD for most of his decades-long career, showed they could successfully use CRISPR to correct the CGD mutation in blood-forming stem cells they’d taken from a few of their patients. While it will take at least a year before those corrected cells can be infused back into the first CGD patient, the researchers have already shown that, when infused into mice, those edited cells can find their way to the bone marrow, where they begin producing fully functioning neutrophils.
De Ravin and Malech are careful to say they are still pursuing other, more conventional gene therapy (“gene therapy 1.0”). Those approaches have been studied for much longer and, after decades of setbacks and slow progress, are finally beginning to show real potential to help patients. But CRISPR, if it can be delivered safely and successfully, would have clear advantages. When a virus inserts a replacement gene into the genome at random sites, as in conventional gene therapy, the replacement gene is not controlled in the same way as the normal gene. Repair of the gene mutation at the gene’s normal site ensures the repaired gene is controlled by the natural control elements that are already there. This ensures that the gene functions in the right places, at the right time, and to the right degree.
“Nature has devised the system to work in an ideal way,” Malech explains. “What gene editing does when it repairs a mutation is essentially to bring the cell back to that ideal …. If one looks at the long view of where we’d like to be in 25 years, it’s not workarounds, but literally correcting the gene so it looks like the normal gene. And that’s what we’ve done here.”
For De Ravin, the fact that her team has been able to use CRISPR to reach right into a cell and seamlessly repair a single base pair out of billions of base pairs in the human genome is nothing short of mind boggling. It’s surely encouraging news for any CGD patient and others with conditions that might be tackled in essentially the same way. Karp realizes that it will take time before the new findings can lead to a clinical trial. Nevertheless, as soon as he saw the results when the study came out earlier this year, he sent De Ravin a text message.
“I’m ready,” he typed. “Are you ready?”
Karp isn’t the only one who’s ready to see CRISPR make its way out of the laboratory and into clinical trials. In fact, CRISPR tools already have made their trials debut in other arenas. Last year, Chinese scientists injected the first patient with T cells they’d edited with CRISPR. While results of the trial aren’t out yet, the cells were programmed to more effectively fight against an aggressive form of lung cancer.
In a report in Nature when news of the Chinese trial broke, Carl June, at the University of Pennsylvania in Philadelphia, predicted the move was “going to trigger Sputnik 2.0, a biomedical duel on progress between China and the United States.” June himself has pioneered an approach to modifying T cells to attack cancer using a variety of tools. After June’s approach passed an initial safety review last summer, he and his group are widely anticipated to launch what may well be the first trial of CRISPR-edited T cells in the U.S., with backing from internet billionaire Sean Parker, a creator of Napster and the first president of Facebook.
As Charlie Gersbach, a professor of biomedical engineering at Duke University, explains, blood cells and, in particular, T cells are the “lowest hanging fruit” when it comes to gene editing. Blood cells are easily modified because they can be taken out of the body, edited in the lab, and then returned to the body via infusion. While it’s possible to edit any blood cell, including blood-forming stem cells, in a similar manner, T cells are a safer place to start because they are committed cells and therefore less likely to become cancerous or otherwise go awry. In fact, by using other approaches, T cells edited to resist HIV infection have been safely returned to the body for years. In January, researchers also reported that T cells edited with a tool known as TALENs had successfully kept two babies with leukemia in remission for a year.
CRISPR promises to enable more of the same, but with even greater ease and precision. The conditions for which CRISPR has the potential to make an impact in the near term include sickle cell disease, hemophilia, HIV, and Duchenne muscular dystrophy. In some cases, there might be multiple ways CRISPR gene editing could correct disease. Take sickle cell, for instance, which was the first to be molecularly characterized and is among the best-known genetic diseases. In patients with sickle cell, abnormal hemoglobin leaves red blood cells misshapen, which can hinder blood flow, causing painful attacks and organ damage. One way to treat the disease is to tackle the sickle cell mutation head on, correcting the broken gene in blood-forming stem cells from patients. But Daniel Bauer from Dana-Farber/Boston Children’s Cancer and Blood Disorders Center is championing another, perhaps easier alternative.
Some people who would otherwise suffer from sickle cell disease are protected because their bodies continue to produce a fetal form of hemoglobin. The amount of fetal hemoglobin that is produced is controlled by a stretch of DNA that acts as a switch. Bauer and his colleagues have shown that they can use CRISPR editing to remove that switch, thereby increasing levels of protective fetal hemoglobin. This approach, though in some ways less direct, has an advantage, because it’s easier to break a gene than it is to correct one. Bauer, who is also an assistant professor of pediatrics at Harvard Medical School, says he hopes to see a clinical trial within the next few years.
“All the pieces are in place and so there’s no need for technologic improvement,” he says. “It should be possible with what exists today. It’s a matter of making sure we have the best possible reagents and protocols to do this in a manner that has the greatest chance for success.”
While blood cells may be more easily accessed, the promise of CRISPR technology surely isn’t limited to them. The company Editas is expected to launch a clinical trial using CRISPR to edit a rare form of blindness out of the retina. According to the company’s latest progress report, if results in non-human primates look encouraging, a trial might begin enrolling human patients as soon as the end of the year. Gersbach recently showed it was possible to use CRISPR to correct Duchenne muscular dystrophy (DMD) in the muscles of mice with an approach that could be readily applied to people if additional studies in larger animals prove safe and effective.
Many also hope that CRISPR can one day be used to eradicate HIV. Recently, researchers at Temple University in Philadelphia successfully removed the HIV virus from infected cells in mice. While a major step forward in finding a cure, some have found obstacles. For example, Chen Liang of McGill University in Montreal made headlines with evidence that HIV could evolve resistance to CRISPR’s cuts in just two weeks. The good news, Liang says, is that researchers have already found a way around this resistance: by clipping the virus in two places instead of one.
Another challenge for CRISPR in general is reach: Can CRISPR-derived healthy genes be delivered efficiently to all of the cells where they are needed in the body? And can they be delivered only to those places? CRISPR still comes with the risk of “off-target effects,” when it creates nicks in parts of the DNA where it shouldn’t.
On the other hand, Bauer points out, radiation and chemotherapies used to treat cancer come with DNA-damaging off-target effects too. Ultimately, scientists will have to minimize the risks of CRISPR as best they can. Then, as with any other treatment, doctors and patients will have to weigh the risks and benefits of CRISPR as demonstrated in clinical trials against the other alternatives.
X-LINKED RECESSIVE INHERITANCE: CARRIER MOTHER
Lake eventually woke up from his medically induced coma with all of his functions fully intact. But with the infections becoming more frequent and his condition more dire, it was time to consider other options. If a suitable donor could be found, a bone marrow transplant offered a chance for a cure, but the procedure would be harrowing. Rachel feared Lake wouldn’t make it through the chemo that would be required to clear the way for donor cells to take hold in her son’s bones, where they could begin to produce working neutrophils. As it turned out, the family couldn’t find a suitable match for him anyway, as is often the case.
Lake didn’t have time to wait for CRISPR; fortunately, he wouldn’t have to. Rachel learned he was a potential candidate for an experimental gene therapy procedure, in which doctors would use a virus — one that’s thought to be more effective and safer than the one Karp received years ago — to deliver a working gene replacement into some of his blood-forming stem cells before giving them back to him. The approach would require chemo to prepare Lake’s body for receiving the modified cells, but it wouldn’t be as aggressive as that needed for a bone marrow transplant.
Lake, now 17, is one of the first patients to receive the treatment — and so far, so good. On Day 187 post-gene therapy, Rachel updated her Facebook followers: “Lake remains extremely well: proven last week with a successful clinic appointment. Bloods were taken and analysed and I am happy to confirm Lake continues to have a stable neutrophil function.”
For the first time in his life, Lake has neutrophils that actually work. Although the gene therapy 1.0 approach can’t make Lake’s neutrophils function at 100 percent in the way CRISPR potentially could, the hope is that they will work well enough. Rachel continues to track the days since Lake received his life-giving infusion of treated cells. He is living at home and has been able to return to college full time. He and his mother can finally spend time together without the pressures of constant doctor visits or having to return home midday for medications.
“It’s given us a lot of freedom,” Rachel says. “Without a perfect bone marrow match, the outcome could be very different. Lake may be [among the first], but I think it’s only a matter of time before a lot more children are cured through gene therapy and gene editing. ”
Karp says he’d like to be one of the first in line if or when a CRISPR trial in CGD opens up. Although his health is relatively stable at the moment, he says that he and his brother are living on borrowed time. The Karp brothers are only in their mid to late 40s, and yet, Karp says, few have lived as long with CGD as they have. Age makes the infections harder to handle, and he wants to see his two healthy children, ages 8 and 11, grow up.
“The correction they saw in the mice was really unheard of, and even something close to that would give us a fully functional immune system,” Karp says. “I’m hopeful — it’s a cautious hope because I realize we still have a way to go — but hopefully this is the breakthrough we’ve been waiting for.”