The Code Breaker, page 22
To an unnecessary extent, the prolonged fight was driven by emotions and resentments. Instead, Doudna and Zhang could have followed the example of Jack Kilby of Texas Instruments and Robert Noyce of Intel who, after five years of wrangling, agreed to share the patent rights for the microchip by cross-licensing their intellectual property to each other and splitting the royalties, which helped the microchip business grow exponentially and define a new age of technology. Unlike the CRISPR contestants, Noyce and Kilby obeyed an all-important business maxim: Don’t fight over divvying up the proceeds until you finish robbing the stagecoach.
I. I am using shorthand when I refer to the applications. When I talk about Doudna’s, I am referring to the ones she did jointly with Charpentier, Berkeley, and the University of Vienna. Likewise, when I talk about Zhang’s applications, I am referring to the ones he did with the Broad, MIT, and Harvard.
PART FOUR CRISPR in Action
If ever man fell ill, there was no defense
—no healing food, no ointment, nor any drink—
but for lack of medicine they wasted away,
until I showed them how to mix soothing remedies.
—Prometheus, in Aeschylus’s Prometheus Bound
Dr. Haydar Frangoul of the Sarah Cannon Research Institute in Nashville with Victoria Gray
CHAPTER 32 Therapies
Sickle cell
In July 2019, a doctor at a Nashville hospital plunged the needle of a large syringe into the arm of a thirty-four-year-old African American woman from a small town in central Mississippi and infused her with stem cells that had been extracted from her blood and edited using CRISPR-Cas9.They were now being reinserted in an attempt to cure her of the sickle-cell disease that had plagued her with debilitating pain since she was a baby. Thus did Victoria Gray, a mother of four children, become the first person in the United States to be treated with a CRISPR gene-editing tool. The clinical trial was led by CRISPR Therapeutics, the company formed by Emmanuelle Charpentier. When Gray was injected, her heart rate shot up and for a while she had trouble breathing. “There was a little scary, tough moment for me,” she told NPR reporter Rob Stein, who was allowed to follow her treatment. “After that, I cried. But it was happy tears.”1
Much of the attention paid to CRISPR these days involves its potential to make inheritable (germline) edits in humans that will be passed along to all the cells of all of our future descendants and have the potential to alter our species. These edits are done in reproductive cells or early-stage embryos. This is what occurred with the CRISPR baby twins in China in 2018, and it is the controversial topic that I will discuss later in this book. But in this chapter I’m going to focus on what will be, at least for now, the most common and welcome uses of CRISPR: cases like that of Victoria Gray, in which CRISPR is used to edit some, but not all, of the body (somatic) cells of a patient and make changes that will not be inherited. This can be done by taking the cells out of the patient, editing them, and returning them (ex vivo) or by delivering the CRISPR editing tool into cells inside of the patient (in vivo).
* * *
Sickle-cell anemia is one of the best candidates for ex vivo gene editing because it involves blood cells that can be easily extracted and returned. The disease is caused by a mutation in a single letter out of more than three billion base pairs of a person’s DNA, which causes a kink in the hemoglobin protein. A normal version of hemoglobin protein forms round and smooth blood cells, able to move easily through our vessels and carry oxygen from our lungs to the rest of our body. But the kinked hemoglobin protein forms long fibers that contort the red blood cells, which causes them to clump together and crumple into the shape of a sickle. Oxygen does not get to tissues and organs, causing severe pain and, in most cases, death by age fifty. Sickle-cell disease afflicts more than four million people worldwide, about 80 percent of them in sub-Saharan Africa, and about ninety thousand people in the U.S., mainly African Americans.
The simplicity of the genetic glitch and the severity of the syndrome make it a perfect candidate for gene editing. In the case of Victoria Gray, doctors extracted stem cells from her own blood and edited them, using CRISPR, to activate a gene that produces a type of blood cell that is normally made only during the fetal stage of life. That fetal-stage hemoglobin is healthy, so if the genetic modification works, patients can start producing their own good blood.
A few months after she was injected with her edited cells, Gray drove up to the Nashville hospital to see if the therapy was working. She was optimistic. Ever since she got the edited cells, she hadn’t needed to get donor transfusions or had any attacks of pain. A nurse inserted a needle and drew multiple tubes of blood. After a nervous wait, her doctor came in to give her the news. “I am super-excited about your results today,” he said. “There are signs that you are starting to make fetal hemoglobin, which is very exciting for us.” About half of her blood was now fetal hemoglobin with healthy cells.
In June 2020, Gray got some even more exciting news: the treatment seemed to be lasting. After nine months, she still had not suffered any sickle-cell pain attacks, nor did she need any further blood transfusions. Tests showed that 81 percent of her bone marrow cells were producing the good fetal hemoglobin, meaning that the gene edits were sustained.2 “High school graduations, college graduations, weddings, grandkids—I thought I wouldn’t see none of that,” she said after getting the news. “Now I’ll be there to help my daughters pick out their wedding dresses.”3 It was an amazing milestone: CRISPR had apparently cured a genetic disease in humans. In Berlin, Charpentier listened to a recording of Gray’s emotional NPR interview. “It was pretty amazing to realize as I heard her,” she says, “that the little baby I helped to create, CRISPR editing, means that she will no longer suffer.”4
Affordability
Applications of CRISPR such as this are likely to be lifesavers. They are also sure to be expensive. In fact, the treatment of a single patient could cost $1 million or more, at least initially. So the prospect of CRISPR doing great good is matched by its potential to bankrupt the healthcare system.
Doudna began to focus on this problem after a discussion that she had with a group of U.S. senators in December 2018. The meeting at the Capitol was held a few weeks after the announcement that twin “CRISPR babies” had been born in China with inheritable edits, and Doudna expected it to focus on that headline-making news. At first it did. But to her surprise, the discussion quickly shifted from the perils of inheritable gene-editing to the promise of using gene editing to treat diseases.
Doudna told the senators that CRISPR was on the verge of creating a cure for sickle-cell disease, which got them to perk up, but they immediately peppered her with questions about the cost. “We have 100,000 people in the U.S. affected by sickle cell,” one senator pointed out. “How are we going to afford that if it’s $1 million per patient? That just breaks the bank.”
Doudna decided that making sickle-cell treatments affordable should become a mission of her Innovative Genomics Institute. “The Senate hearing was, for me, a watershed moment,” she says. “I’d been thinking a lot about costs before that, but not in a focused way.” When she arrived back at Berkeley, she convened a series of meetings of her team to discuss how to make wide access to sickle-cell treatments a new core part of their mission.5
The public-private partnership that led to the availability of the polio vaccine became an inspiration. She reached out to the Gates Foundation and the National Institutes of Health, which announced a partnership for a Cure Sickle Cell Initiative funded with $200 million.6 The primary scientific goal of the initiative is to find a method to edit the sickle-cell mutation inside of a patient without needing to extract bone marrow. One possibility is to inject into the patient’s blood a gene-editing molecule with an address label that directs it right to the cells in the bone marrow. The difficult part will be to find the right delivery mechanism, such as a virus-like particle, that won’t trigger the patient’s immune system.
If the initiative is successful, it will not only cure a lot of people of a dreadful disease; it will advance the cause of health justice. Most sickle-cell patients in the world are Africans or African Americans. These are populations that have been historically underserved by the medical community. Even though the genetic cause of sickle-cell disease has been understood for longer than any similar disorder, new treatments have lagged behind. For example, the fight against cystic fibrosis, which affects primarily white Americans and Europeans, has received eight times more funding from government, charities, and foundations. The great promise of gene editing is that it will transform medicine. The peril is that it will widen the healthcare divide between rich and poor. Doudna’s sickle-cell initiative is designed to find ways to avoid that.
Cancer
In addition to treating blood disorders, such as sickle-cell anemia, CRISPR has been used to fight cancer. China has been the pioneer in this field, and it is two or three years ahead of the United States in devising treatments and getting them into clinical trials.7
The first person to be treated was a lung-cancer patient in Chengdu, a city of 14 million in the western Chinese province of Sichuan. In October 2016, a team removed from the patient’s blood some of his T-cells, which are the white blood cells that help fight off diseases and confer immunity. The doctors then used CRISPR-Cas9 to disable a gene that produces a protein, known as PD-1, which stops the cell’s immune response. Cancer cells sometimes trigger the PD-1 response, thus protecting themselves from the immune system. By using CRISPR to edit the gene, the patient’s T-cells become more effective in killing the cancer cells. Within a year, China had seven clinical trials using this technique.8
“I think this is going to trigger ‘Sputnik 2.0,’ a biomedical duel on progress between China and the United States,” said Carl June, a noted cancer researcher at the University of Pennsylvania who at the time was still struggling to get regulatory approval for a similar clinical trial. He and his colleagues were finally able to get their trial underway and reported preliminary results in 2020. Their method, used in three late-stage cancer patients, was more sophisticated than the one used in China. They knocked out the PD-1 gene and also inserted into the T cells a gene that targeted the patients’ tumors.
Although the patients were not cured, the trials showed that the technique was safe. Doudna and one of her postdoctoral students published an article in Science explaining the Penn results. “Until now, it has been unknown whether CRISPR-Cas9–edited T cells would be tolerated and thrive once reinfused into a human,” they wrote. “The findings represent an important advance in the therapeutic application of gene editing.”9
CRISPR is also being used as a detection tool to identify precisely what type of cancer a patient has. Mammoth Biosciences, a company that Doudna founded with two of her graduate students, is designing diagnostic tools based on CRISPR that can be used on tumors to identify quickly and easily the DNA sequences associated with different types of cancers. Then precision treatments can be tailored for each patient.10
Blindness
The third use of CRISPR editing that was underway by 2020 was to cure a form of congenital blindness. In this case the procedure was performed in vivo—inside the patient’s body—because eye cells cannot be extracted and returned the way blood and bone marrow cells can. The clinical trials were conducted in partnership with Editas Medicine, the company founded by Zhang and others.
The goal was to treat Leber congenital amaurosis, a common cause of childhood blindness. Those with the condition have a mutation in the gene that makes light-receptor cells in their eye. It causes a critical protein to be shortened, so that the light that hits the cells is not converted into nerve signals.11
The first use of the treatment occurred in March 2020, just before coronavirus shut down most clinics, at the Casey Eye Institute in Portland, Oregon. In the hour-long procedure, doctors used a tiny hair-width tube to inject three drops of fluid containing CRISPR-Cas9 into the lining that contains light-sensing cells directly beneath the retina of the patient’s eyes. A tailored virus was used as the delivery vehicle to transport the CRISPR-Cas9 into the targeted cells. If the cells are edited as planned, the fix will be permanent, because unlike blood cells, the cells of the eye do not divide and replenish themselves.12
Coming soon
Work is also underway on some more ambitious uses of CRISPR gene editing that could make us less vulnerable to pandemics, cancers, Alzheimer’s, and other diseases. For example, a gene known as P53 encodes for a protein that suppresses the growth of cancerous tumors. It helps the body respond to damaged DNA and prevents cancerous cells from dividing. Humans tend to have one copy of this gene, and cancers proliferate if something goes wrong with it. Elephants have twenty copies of this gene, and they almost never get cancer. Researchers are currently exploring ways to add an extra P53 gene into humans. Likewise, the gene APOE4 raises the risk of the devastating disease of Alzheimer’s. Researchers are looking for ways to convert it into a benign version of the gene.
Another gene, PCSK9, encodes for an enzyme that facilitates the creation of LDL, the “bad” cholesterol. Some people have a mutated copy of the gene that leads to very low levels of this cholesterol, which results in an 88 percent reduction in risk for coronary heart disease. Before he decided to edit the gene for HIV receptors in the CRISPR babies he created, He Jiankui was studying ways to use CRISPR to make germline edits in the PCSK9 gene of embryos to produce designer babies with far less risk of having heart disease.13
At the beginning of 2020, there were two dozen clinical trials for various uses of CRISPR-Cas9 in the pipeline. They included potential treatments for angioedema (a hereditary disease that causes severe swelling), acute myeloid leukemia, super-high cholesterol, and male pattern baldness.14 In March of that year, however, most academic research labs were temporarily shut down because of the coronavirus pandemic. An exception was made for labs that were engaged in fighting the virus. Many CRISPR researchers, Doudna foremost among them, would shift their focus to creating detection tools and treatments for the disease, some of them making use of the tricks they had learned from studying how bacteria developed an immune response to ward off new viruses.
Josiah Zayner
CHAPTER 33 Biohacking
Wearing a black T-shirt and tight white jeans, Josiah Zayner stood in front of a roomful of biotechnologists at the Global Synthetic Biology Summit in San Francisco in 2017 and launched into a pitch about a do-it-yourself “frog genetic engineering kit” that he made in his garage. Available online for $299, it allowed users to cause a frog’s muscles to double in size in a month by injecting CRISPR-edited DNA that turned off the gene that produces myostatin, a protein that inhibits muscle growth once an animal has reached its mature size.
It would also work on humans, Zayner said, flashing a conspiratorial smile. You could grow bigger muscles.
There was some nervous laughter and then a few shouts of encouragement. “What’s holding you back?” someone hollered.
Zayner, a serious scientist wrapped in the persona of a rebel, took a swig of Scotch from a leather-covered hip flask. “Are you suggesting I should try it?” he responded.
There were more murmurs, a few gasps and laughs, then some more encouragement. Zayner reached into a medicine bag, pulled out a syringe, filled it from a vial of the edited DNA, and proclaimed, “All right, let’s do it!” Sticking the needle into his left forearm, he winced a bit and then plunged the liquid into his veins. “This will modify my muscle genes to give me bigger muscles,” he proclaimed.
There was scattered applause. He took another swig of Scotch from his hip flask. “I will let you know how it works out,” he said.1
* * *
Zayner, with his bleached-blond forelock and ten piercings in each ear, thus became the poster boy for a new breed of biohacker, the spirited band of renegade researchers and merry hobbyists who want to democratize biology through citizen science and bring its power to the people. While conventional researchers worry about patents, biohackers want to keep the bio-frontier free of royalties, regulations, and restraints, similar to the way digital hackers felt about the cyber-frontier. In most cases, the biohackers are, like Zayner, accomplished scientists who forgo working at universities or corporations and instead become the rogue wizards of a rarefied part of the do-it-yourself maker’s movement. In the drama of CRISPR, Zayner plays the role of one of Shakespeare’s wise fools, such as Puck in A Midsummer Night’s Dream, who speaks truth under the guise of showmanship, pokes fun at the pretensions of the high-minded, and pushes us forward by pointing out what fools these mortals be.
As a teenager, Zayner worked as a programmer for Motorola’s cell phone network, but he got laid off when the tech bubble burst in 2000, so he decided to go to college. He earned his bachelor’s degree in plant biology from Southern Illinois University and a doctorate in molecular biophysics at the University of Chicago, where he studied how light-activated proteins work. Instead of doing traditional postdoc studies, he wrote about using synthetic biology to help colonize Mars and found himself recruited to work for NASA. But he was not cut out for a hierarchical organization, so he quit to pursue the freedom of being a biohacker.
Before getting into CRISPR, Zayner tried a variety of synthetic biology experiments, including on himself. To treat his gastrointestinal problems, he performed a fecal transplant (don’t ask) to transform his gut’s microbiome. He did the procedure in a hotel room with two filmmakers documenting the scene, and (in case you really do want to know how it works) it became a short documentary called Gut Hack that can be found online.2
