Editing Humanity: The CRISPR Revolution and the New Era of Genome Editing

CHAPTER 12 FIX YOU

In April 2016, Sean Parker, the billionaire co-founder of Napster portrayed by Justin Timberlake in the film The Social Network, hosted a star-studded party at his $55 million Los Angeles home, which borders the Playboy Mansion. Among the celebrities in attendance were Tom Hanks, Peter Jackson, Sean Penn, “Mother of Dragons” Emilia Clarke, and Katy Perry. Musical performances included John Legend, the Red Hot Chili Peppers, and Lady Gaga slaying a rendition of “La Vie en Rose.”¹ In the audience, Bradley Cooper was blown away, “like in that old Maxell cassette commercial,” he said. That performance clinched her starring role in Cooper’s remake of A Star is Born.

Parker was celebrating the launch of the Parker Institute for Cancer Immunotherapy (PICI), to which he personally pledged $250 million. The guest list also included medical talent from cancer centers in LA, San Francisco, New York, Philadelphia, and Houston. Two years after the launch party, PICI supported Carl June’s team at the University of Pennsylvania Abramson Cancer Center in treating the first cancer patients in a CRISPR trial.² A Phase I trial is all about safety, but June is well aware that Chinese doctors are pushing ahead much faster. “We are at a dangerous point in losing our lead in biomedicine,” June told the Wall Street Journal.³

The SINATRA trial^I is an extension of June’s pioneering work on CAR-T cells, arming the patient’s own T cells to hunt tumor cells. Cancer patients are alive today because of these first-generation immunotherapies, but there is room for improvement. June’s team performed three kinds of CRISPR gene edits: insertion of a gene into the patients’ T cells that codes for a protein engineered to detect cancer cells while simultaneously removing the gene that interferes with this process. The third edit removes a gene that marks the T cells as immune cells and thus prevents the cancer cells from disabling them. Once edited, the manipulated cells are re-administered to the patient.

June’s team published the initial results on three very ill patients who had endured multiple rounds of chemotherapy and bone marrow transplantation in February 2020.⁴ The CRISPR therapy appeared safe—no toxicity, no cytokine storms, no neurological toxicity. June was relieved that there had been no adverse immune responses given the bacterial origin of Cas9. And while there was a low level of chromosomal rearrangements, he said that was similar to what astronauts who have been in space a few months endure.⁵

The journal Science treated the report as another major milestone. The cover headline read: HUMAN CRISPR.

Genome editing offers two enticing benefits for patients: first, it strikes at the root cause of a disease by correcting the code, repairing the faulty DNA sequence. Conventional drugs typically treat symptoms, not the root cause of a disease. Traditional gene augmentation therapy (as discussed in the previous two chapters) might compensate for, but does not repair, the underlying mutation. Second, the fix should in principle last forever, a one-and-done repair rather than chronic disease management. Of course, the CRISPR machinery still has to be delivered to the right tissues, safely, without triggering the patient’s immune system or causing any collateral DNA damage. None of those issues has been completely resolved, but the precision and safety of CRISPR is improving all the time, as can be seen in some of the early results in clinical trials.

A decade ago, the prospect of a universal cure for sickle-cell disease (SCD) didn’t look hopeful. But now genome-editing strategies are showing promise, adding to various approaches—allogeneic stem cell transplant, gene therapy, derepressing γ-globin—discussed in the previous chapter, at least for patients in first-world countries.

In April 2019, Sangamo announced results for their first patient treated with an ex vivo gene-edited cell therapy, in which ZFNs disrupt the BCL11A enhancer in the patient’s hematopoietic stem cells to boost γ-globin production. “I could not have imagined HbF this high in my wildest dreams,” tweeted Sangamo alumnus Fyodor Urnov. “Thirty-one percent HbF is SPECTACULAR.” Meanwhile, studies by Merlin Crossley’s group in Sydney are developing an approach he calls “organic gene therapy,” using CRISPR-Cas9 to recapitulate specific HPFH mutations to boost HbF levels.⁶

Stanford’s Matthew Porteus has been on a quest to use genome editing in the clinic since the early 2000s.⁷ Using CRISPR-Cas9 to break the DNA before fixing the sequence, Porteus says, is like fixing the headlight on someone’s car by first busting the headlight with a hammer before repairing it. The goal is to ensure that about 20 percent of the stem cells repopulating the bone marrow are genetically fixed. That means harvesting some 500 million stem cells from any given patient. In a specialized facility, those cells are mixed with Cas9 and the AAV vector. The modified cells will be transplanted back into patients, after they have recovered from chemotherapy to make room for the modified stem cells. The biggest hurdle is to improve the efficiency of delivering the Cas nuclease into the appropriate cells.

“We’ll cure people who have sickle-cell disease, not because they have a genetic defect but because they’re human beings and deserve all the rights, responsibilities, and value we should confer on any human being,” Porteus says.⁸ He calls genome editing “an anti-eugenics program.” The eugenics movement in the 20th century was designed to improve the gene pool by sterilizing or eliminating people who had genetic defects. A consequence will be that the frequency of the SCD variant will increase in the population, because now “we’ll be taking people who normally die in childhood and allowing them to live to adulthood, have families.” But it’s a fair exchange, he says. “We should embrace this consequence.”

One of the patients in Porteus’s care is teenager David Sanchez, who charms with his eloquence and humor. “My blood just doesn’t like me very much, I guess,”⁹ he shrugs as he prepares for his monthly three-hour appointment with the apheresis machine, which replaces his warped erythrocytes with a fresh batch of healthy biconcave blood cells. His nurse likens David’s visit to booking an oil change for a car. David endures his share of debilitating pain episodes but he exhibits no self-pity, even after enduring brain surgery. “I’m not just going to not play basketball. You can’t not play basketball,” he says in the film Human Nature.

Asked what he thinks about the possibility of fixing his disease using CRISPR, potentially eradicating the scourge of sickle cell altogether, Sanchez says, “Hmmn… that sounds cool.” Then he pauses. “There’s a lot of things that I learned having sickle cell,” including patience and keeping a positive outlook. “I don’t think I’d be me if I didn’t have sickle cell.”

A new biotech industry is rising fast in the belief that genome editing will provide the ultimate new weapon to deliver precision medicine. The industry is centered in Kendall Square, where the first three publicly traded CRISPR genome editing companies—Editas Medicine, CRISPR Therapeutics, and Intellia Therapeutics—jostle for space and research talent with dozens of innovative biotech and gene therapy firms.

In July 2019, CRISPR Therapeutics (working with Vertex Pharmaceuticals) became the first company to launch a CRISPR-based clinical trial for a genetic disease in the United States. A thirty-four-year-old mother of four from Mississippi, Victoria Gray, was the first of dozens of volunteers in the trial. Diagnosed with SCD as a baby, her faith has sustained her during tough times. “I always knew that something had to come along and that God had something important in store for me,” she told National Public Radio’s Rob Stein.¹⁰ At a clinical center in Nashville, Tennessee, doctors removed her bone marrow cells and administered chemotherapy. On July 2, 2019, hematologist Haydar Frangoul injected some two billion of Gray’s gene-edited “supercells” back into her body.

After weeks in hospital, Gray was finally able to return home, leaving hospital wearing a blood-red T-shirt with I AM IMPORTANT emblazoned on the front and proudly sporting an invisible genetic modification. “I’m a GMO. Isn’t that what they call it?” she said.¹¹ A month later, she returned to Nashville to receive her preliminary results, this time modeling a black sweatshirt that said simply, WARRIOR. Frangoul could not disguise his excitement.¹² Almost half of Gray’s hemoglobin consisted of the fetal form, a spectacular result. That was still the case nine months after her therapy, with 80 percent of her bone marrow cells displaying the desired edit. Another patient with beta thalassemia in Germany has not needed a blood transfusion in fifteen months.¹³ But it is still too soon to call it a cure.

CRISPR Therapeutics was the brainchild of Emmanuelle Charpentier. “I always had in mind that one day it would be nice if my research could lead to anti-infective strategies,” she told me. “But the right application for me was human gene therapy.”¹⁴As she was setting up her new lab in Berlin, Charpentier called her old friend, Rodger Novak, an executive at Sanofi who had been a postdoc with her at Rockefeller in the mid-’90s. “What do you think about CRISPR?” she asked. Novak didn’t know what she was talking about. He suggested Charpentier talk to an investor friend, Shaun Foy, to appraise the technology. “Maybe you think I’m crazy?” Charpentier asked Foy. A month later, Foy called Novak with a simple suggestion: “You need to leave your job!” he said.

Charpentier partnered with Novak and Foy to create Inception Genomics in November 2013, which later became CRISPR Therapeutics. They initially selected Basel, Switzerland, as their pharma-friendly headquarters before relocating to Kendall Square for closer access to investors and talent. (They also founded another company, ERS Genomics—the name assembled from the initials of the three cofounders—to handle Charpentier’s patent rights.) Charpentier had initially approached Doudna and Zhang about potentially teaming up to form a CRISPR company. Doudna demurred, agreeing instead to join forces with George Church and Zhang. Two other big names in Boston joined the band: Keith Joung, a pathologist at Mass General Hospital who had deep experience working on zinc fingers, and David Liu, a Harvard chemistry professor and Zhang’s friend at the Broad Institute. The company’s initial name was Gengine, but it was sensibly retired in favor of something with a bit more, um, gravitas: Editas Medicine.

The all-star quintet met in Boston for a company photoshoot but by the time Editas was announced, something appeared to have gone awry. One reporter noted that Doudna was notably absent from the official photos, a wisp of auburn hair in one photo the only evidence she’d been there at all. The reason soon became apparent: The Broad Institute had scooped Doudna and Charpentier by expediting Zhang’s patent application. In May 2014 Zhang was awarded the big CRISPR-Cas9 patent. Doudna quickly cut ties with Editas. She later offered family reasons and the burden of travel, but the patent defeat, even if only the first round of a marathon contest, stung.

Editas was backed by three giant venture capital firms working together for the first time—Polaris, Flagship and Third Rock. Bill Gates joined the second round of investors who put up more than $100 million. Gates was fascinated by the potential of genome editing not only to treat genetic diseases but also to combat infectious diseases such as malaria and improve food production in developing nations.¹⁵ As CEO Editas appointed Katrine Bosley, who had spent twenty-five years in biotech, most recently as chief executive of a cancer drug company, Avila Therapeutics, which is where I first met her.¹⁶ When Bosley^II first heard about genome editing, it sounded like science fiction. But during a few months as an entrepreneur-in-residence at the Broad Institute, she got to know Zhang and learn about CRISPR’s potential. She was impressed by the technology’s ease of use and wide applicability—something in common with the novel chemistry her team developed at Avila.^III

The lead program at Editas is for another form of Leber’s congenital amaurosis (LCA type 10). The attraction of LCA10 as a target was for many of the same reasons that Bennett identified: because the eye is both small and accessible as a delivery target. Moreover, the desired gene edit—a small deletion—has a lower degree of difficulty. LCA10 is caused by a single-letter mutation in a gene called CEP290, first characterized in a consanguineous French-Canadian family. CEP290 is expressed in the photoreceptors behind the retina; in LCA10 patients, the loss of the protein leads to degeneration of the outer segment of the photoreceptors. The LCA10 mutation, which resides in an intron that is normally spliced out of the gene transcript, results in an extra chunk of sequence being inserted into the RNA message. This cryptic exon includes a premature stop codon: so all of these RNA messages fail to produce a functional protein.

The Editas plan is to use CRISPR-Cas9 to deliver a pair of precise cuts flanking the mutation to restore normal gene splicing, thus producing the normal protein and rebuilding the photoreceptors. Like Spark Therapeutics, Editas uses an AAV vector to deliver the CRISPR machinery, dubbed EDIT-101. In July 2019, together with Allergan, Editas announced enrollment of the first patients in the Brilliance clinical trial.¹⁷ The first surgery was performed in an hour-long procedure at the Casey Eye Institute at the Oregon Health & Science University in Portland in early 2020. It was called a new era in medicine—the first time CRISPR had been injected directly into a human patient, as opposed to the ex vivo approach employed for Victoria Gray.¹⁸

In early 2019, Bosley surprisingly stepped down as CEO. During her career, she had experienced the thrill of seeing drugs impact patients’ lives, but she was foregoing that opportunity at Editas. (She did admit in one interview that five years at the helm seemed like a thousand.) She signed off on Twitter saying: “I’m proud of everything we achieved and built together, and I’ll always be cheering them on—now as Editas Emeritas, as we say.”

In late 2013, Nessan Bermingham, a rambunctious venture capitalist with Atlas Venture, conceived a new gene editing company. Bermingham grew up on an army base in County Kildare. After earning his PhD in London at St Mary’s Hospital Medical School—something we have in common—he did postdoctoral research at Baylor College of Medicine before moving into finance. During an Atlas retreat in Miami, Bermingham struck up a conversation at the salad bar with John Leonard, a physician who had just retired after a successful career in big pharma.

Leonard moved to industry early in his career after his wife was diagnosed with multiple sclerosis. In the early 1990s, he ran the antiviral program at Abbott Laboratories during the AIDS crisis. “Our mission was absolute, and from that I learned how empowering belief can be,” he said.¹⁹ His team developed ritonavir, one of the first HIV protease inhibitors, and later Humira. After retiring as head of R&D at AbbVie in 2013, he dabbled in a couple of more low-key entrepreneurial ventures, including a craft cider company in Michigan. The trip to Miami was just a networking opportunity, or so he thought. A few months later, Bermingham flew to Chicago to take Leonard to lunch and lay out his ideas for Intellia Therapeutics. (The company’s name came from the Greek “entelia,” a state of pristine excellence.) “I couldn’t think of a more promising and exciting technology than CRISPR,” he said. Bermingham was confident he could secure Doudna’s intellectual property (IP), which was good enough for Leonard, who joined as chief medical officer.²⁰

In May 2014, Bermingham officially founded Intellia as CEO in partnership with Doudna’s first company Caribou,^IV which holds Doudna’s IP (and owns a stake of Intellia). Intellia’s cofounders include Barrangou, Sontheimer, and Marraffini. Caribou is led by Rachel Haurwitz, who was the first student in Doudna’s lab to work on CRISPR, but determined to launch a biotech company even before she finished her thesis. The other cofounders were Jínek and James Berger (now at Johns Hopkins).

Intellia emerged from stealth six months later, with support from Novartis before another round raised $70 million. In May 2015, officially divorced from Editas, Doudna joined the cofounder group along with stem cell biologist Derrick Rossi. A year later, Intellia went public, outperforming Editas by reaping some $110 million in the largest IPO for a Boston biotech that year. Haurwitz and Barrangou joined the team celebration as Bermingham ran the opening bell on the Nasdaq exchange.

Bermingham is a fierce competitive athlete, reveling in ultramarathons, boxing, and mountain biking. During an after-dinner speech at a medical conference in Washington, DC, in 2017, Bermingham drew parallels between extreme sports and precision medicine, presenting his vision to develop a one-and-done treatment paradigm where “freedom from genetic disorders is no longer an inherited privilege.” His motivation came from the patients he hoped one day to cure:

When I climb a hill in the final stages of a marathon, I push through because I know that my lungs will never have to fight harder for oxygen than those patients living with alpha-1 lung disease. When I step into the boxing ring, I’m fearless because I know that I’ll not experience the pain children with sickle-cell disease fear every day. When continuing the race demands I choose to suffer, I remind myself it is by my choice and I will never have to face a preventative double mastectomy and living under the sword of breast cancer.²¹

Bermingham needed every piece of inspiration six month later competing in his first Roving Race in Patagonia. Athletes run twenty-five miles for four consecutive days, followed by a fifty-mile overnight leg and a trivial six miles on the final day, while carrying their own gear.²² He placed in the top half out of more than three hundred competitors (dozens of whom didn’t finish) in a time of thirty-nine hours—only nineteen hours behind the winner. Barrangou, no slouch as an entrepreneur, can only doff his hat. “Ness scares me! I can run with those guys, but this guy’s in a different league,” he laughed.

Perhaps exhausted, Bermingham resigned^V as Intellia’s CEO a short time later, passing the torch to Leonard. Barrangou thinks he’s the ideal CEO: “John has done it before. It’s not about being first in the clinic, it’s about being best in the clinic.”²³

Intellia’s biggest bet is on a liver disease called transthyretin amyloidosis (ATTR), which affects about 50,000 patients worldwide. (In 2016, Regeneron paid Intellia $75 million for rights in ten therapeutic areas, including ATTR.) This disease is adult-onset, typically fatal, caused by toxic amyloid protein deposits leading to heart failure and neuropathy. Patients typically survive just a few years after diagnosis. The plan is to use CRISPR-Cas9 to deactivate the TTR gene in the liver using a lipid nanoparticle for delivery, which unlike some viruses does not trigger an immune response. The strategy avoids leaving Cas9 hanging around too long, minimizing the risk of any off-target mistakes. If results in nonhuman primates hold up, this could represent a cure for patients with ATTR.

Eric Olson, a professor at the University of Texas, may not be an expert in genome editing, but he knows muscle.²⁴ Olson started his own lab in the early 1980s at MD Anderson Cancer Center, and taught himself molecular biology. His first two grant applications were trashed by reviewers but it was third time lucky. Olson receives letters and emails almost daily from parents searching for hope, if not a cure, for muscular dystrophy. Olson’s company, Exonics, is on course to make a difference.

Duchenne muscular dystrophy (DMD) is the most common and severe form of inherited muscular dystrophy. It is caused by one of thousands of different mutations in the largest gene in the human genome. As an X-linked disease, DMD affects mostly boys—about 300,000 around the world. The corresponding protein, dystrophin, sits under the membrane of muscle cells and acts like a giant shock absorber; without it, the membranes start to leak, resulting in muscular weakness. Replacing dystrophin is a formidable task, but attempts to find a workaround, such as supplying a “mini” dystrophin gene or switching on a dormant related protein called utrophin, have met with little success.

The dystrophin gene consists of seventy-nine coding sequences, or exons, spread over 2.6 million letters on the X chromosome. Many of the 4,000 catalogued DMD mutations congregate in the middle of the gene between exons 45–50. These frequently result in a “frameshift” mutation, shifting exon 51 out of frame, which in turn compromises production of dystrophin. Interestingly, the middle portion of dystrophin—the spring, if you will—is less critical than the ends of the giant protein. We know this because patients with a milder form of DMD, Becker muscular dystrophy, have shortened springs but otherwise a partially functional protein, and have a longer life expectancy than DMD patients.

Olson’s plan essentially is to use CRISPR to convert some of the DMD mutations in the central exons to the milder Becker form of muscular dystrophy. By using CRISPR-Cas9 to engineer a cut in exon 51 to excise one particular mutation, the resulting protein should be close to fully functional. Just as Jean Bennett found a canine model to test her gene therapy for LCA, Olson’s team turned to another canine model. The beagle colony at the Royal Veterinary College near London looks and sounds as happy and healthy as their normal cousins, with tricolor coats and a trademark howl. But the affected dogs noticeably drag their hind legs.^VI

Leading the Exonics team is an expat from Moldova, Leonela Amoasii. The initial results in 2018 put a smile on everyone’s face.²⁵ Amoasii treated one-month-old puppies and then compared results with controls two months later. The muscle fibers of the treated dogs express newly restored dystrophin protein, as much as 80 percent of normal. But the most compelling evidence is to watch the treated dogs run, jump, and play as happily as their wild-type cousins. “We’re really excited,” says Amoasii. So too is Vertex Pharmaceuticals, which acquired Exonics in June 2019 in a deal potentially worth up to $1 billion—not bad for a company founded less than three years earlier.

For any company hoping to treat a patient with CRISPR genome editing, safety is perhaps the biggest concern. The technology relies on a bacterial enzyme that can slice and dice DNA. Several safety issues have surfaced that have given investigators—and occasionally investors—pause. The biggest concern is that Cas9, while roaming the genome to find the correct target gene, could accidentally latch onto a closely related sequence, perhaps with just a single mismatched base, and cleave in the wrong place. This molecular mistaken identity could be harmless, seamlessly patched up by the DNA repair network. Or it could be disastrous, deactivating a critical gene or potentially switching on a cancer-causing gene. That could mean the end not only of a promising clinical trial but worse, a devastating setback for the entire field.

These concerns are not unique to CRISPR: any programmable genome editor will have a slight chance of fixating on the wrong sequence. But the stakes are higher with CRISPR because of its widespread use and stratospheric expectations. Some off-target fears have been overblown. A study from a Stanford group documenting multiple off-targets in 2018 raised alarms, even though the data were collected on just three lab mice. Industry scientists and academic groups swiftly rebutted any notion that CRISPR-Cas9 was unsafe.²⁶ Subsequent studies suggested that if unintended edits do occur, they are no more frequent than those that inevitably result from background radiation and the errors that naturally accumulate during DNA replication and cell division.

Scientists have devised many ways to improve on-target specificity, from the design of the guide RNA to the choice and design of Cas9 nucleases.²⁷ Concerns were also raised about on-target effects: Allan Bradley, a highly respected mouse geneticist and former director of the Sanger Institute, prompted another mini CRISPR crisis when his group showed that CRISPR-Cas9 can cause larger deletions than expected at the target site.²⁸ Barrangou summed up the sentiment: “Keep calm and CRISPR on!”

Another safety issue is anticipating what happens when a bacterial protein is injected into patients. Porteus and colleagues found that many individuals carry antibodies to Cas9, suggesting they have been previously exposed to bacteria that express the protein.²⁹ This is not surprising; after all, the immune system is designed to detect foreign proteins. A variety of methods—including selecting Cas9 enzymes from different bacteria or modifying the surface of the protein to make it less immunogenic—should minimize the risk of an undesirable immune response.³⁰

Yet another scare flared up in 2018, when two highly publicized reports suggested that genome editing with CRISPR might increase the risk of genomic instability and cancer predisposition by selecting against the function of p53, the most frequently mutated tumor suppressor gene. Among many commentaries mulling over the significance of these findings was David Lane, who dubbed p53 “the Guardian of the Genome.” Lane and Teresa Ho said that this episode was a “cautionary rather than apocalyptic tale,” just like “every therapeutic endeavor of the past and future.”³¹ The case for using genome editing as part of a life-saving T-cell transplant in a 75-year-old cancer patient might be very different to editing cells to correct a Mendelian gene defect in a baby.

These issues were mostly taken in stride by the CRISPR companies. By July 2020, the big three biotechs had a combined market cap of $10 billion. And yet, the question of who actually owned the rights to the invention of the CRISPR revolution was still unresolved.

I. PICI likes to name its clinical trials after famous musicians. Along with Sinatra, it is also organizing trials named after Prince, Gustav Mahler, Cole Porter, Mozart (“Amadeus”), and country music star Tim McGraw, a longtime cancer research advocate.

II. Bosley’s father, Richard Bosley, designed and built the iconic Bosley GT MK I sports car in the 1950s.

III. Avila Therapeutics developed drugs that bind covalently to their target, which is unconventional in drug discovery.

IV. Caribou is an abbreviation for CRISPR-associated ribonucleic acid; the company logo sports a pair of antlers in the shape of a single-guide RNA.

V. Bermingham has since launched a new company called Triplet Therapeutics, a start-up targeting diseases like Huntington’s disease, which are caused by the expansion of triplet repeat DNA sequences.

VI. The dystrophin mutation was first observed in a Cavalier King Charles Spaniel, then bred into a line of beagles, which provide a better physiological match to humans.