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The lucky break behind the first
CRISPR treatment
Gene editing for sickle-cell is here. This is how
researchers knew what DNA to change.
The world’s first commercial gene-editing treatment is set
to start changing the lives of people with sickle-cell disease. It’s
called Casgevy, and it was approved last month in the UK. US approval is
pending this week.
The treatment, which will be sold in the US by Vertex
Pharmaceuticals, employs CRISPR, the Nobel-winning molecular scissors that have
had journalists scrambling for metaphors: “Swiss Army knife,” “molecular
scalpel,” or DNA copy-and-paste. Indeed, CRISPR is revolutionary because
scientists can so easily program it to cut DNA at precise locations they
choose.
But where do you aim CRISPR? That’s the
lesser-known story of the sickle-cell breakthrough. The disease is caused by
faulty hemoglobin, the molecule that carries oxygen in the blood. To cure it,
though, Vertex and its partner company, CRISPR Therapeutics, aren’t fixing the
genes responsible for the mutation that leaves those molecules misshapen.
Instead, the new treatment involves a kind of molecular bank shot—an edit that
turns on fetal hemoglobin, a second form of the molecule that we have in the
womb but lose as adults.
You can think of how the edit works as a kind of double
negative. It adds a misspelling to the turbo-booster of another gene, BCL11A,
that is itself what inhibits the production of fetal hemoglobin in adult
bodies. Without that booster, there’s less inhibition, and more fetal
hemoglobin. Got it?
“When you inhibit the enhancer, you inhibit the inhibitor,”
says Daniel Bauer, a professor at Boston Children’s Hospital and Harvard
University, who helped work it out. “It is kind of complicated.”
The important thing is a happy ending—and this edit really
works. Some patients say they lived in fear of dying, either from an acute
attack of sickling (when their red blood cells start blocking vessels) or from
slow, insidious organ damage. Now early volunteers say
they’re grateful—and, after living with disease their whole lives, even a
little shocked—to be cured.
Newborn theory
The idea that fetal hemoglobin can protect against the
disease is an old one. Sickle-cell is most common in people with African
ancestry. A doctor on Long Island, Janet Watson, had noticed in 1948 that
newborns never showed its signs—the main one being misshapen, crescent-shaped
red blood cells. That was pretty odd for an inborn condition.
“Sickle-cell disease should occur in infancy as often as
later in life,” Watson wrote. But since it didn’t, Watson hypothesized
that the fetal form of the molecule, active in the womb, was protecting babies
for a few months after birth, until it was replaced by the adult version: “The
theory that at once presents itself is that fetal hemoglobin is unable to
produce sickling.”
She was right. But it took another six decades to learn how
the switch-over worked—and how to flip it back. Many of those discoveries were
made in the laboratory of Stuart Orkin, a Harvard researcher who published his
first paper in 1967 and who’s lived through several eras of research on blood
diseases, starting near the dawn of molecular biology.
“I am one of the last men standing,” Orkin told me with a
grin when I met him for a corned-beef sandwich.
Stuart Orkin analyzing DNA from individuals with blood
disorders in his lab in 1985.
He’s a clever scientist who a long time ago decided to study
how the blood system is regulated. Logistically, it was a great topic; blood
cells are easy to get hold of and study.
“I like to solve a problem, and here is a problem that could
be solved,” Orkin says. “How does the system work, and then can you do anything
about it?”
Special sauce
Bill Lundberg, the former chief scientific officer of CRISPR
Therapeutics, the biotech that first started developing the treatment eight
years ago (Vertex later joined as a partner), says the company’s sickle-cell
project directly made use of Orkin's findings. “Stu’s role is really
underappreciated,” he says. “In the space of a few years, his lab did a series
of experiments, each time with a new student—every one of them published in
Science or Nature. That was ultimately the special sauce that we ended up
using.”
Given the media accolades for CRISPR editing, many people
don’t realize it’s really best at ripping scars into genes, not making stylish
rewrites (although that is
coming). For the early CRISPR startups, this meant finding genes to
disable. What could they break in the genome in order to reverse an illness?
Three companies—Editas, Intellia, and CRISPR
Therapeutics—each won big backing from venture capitalists around 2014. For
those start-ups, just contemplating changing people’s genomes seemed radical
enough. “What I said was: Let’s not solve the world’s problems. Let’s simplify.
Let’s ask where it is that human genetics teaches us that if we make
the edit, we cure the disease,” Lundberg recalls about his meetings with the
company founders. “And that is where 50 years of research on fetal hemoglobin
came in.”
Sickle-cell was an attractive target. It’s the most common
serious inherited genetic disease in the US. What’s more, the stem cells that
make red and white blood cells can be removed from a person’s body and then put
back, in what’s known as a bone marrow transplant. That would avoid the need to
use complex technologies to deliver the treatment to people’s bodies. It could
all be done in a laboratory.
VERTEX
That’s exactly how the Vertex treatment works. Some of a
patient’s stem cells are removed from the blood with a filtering machine, and
the CRISPR cutting protein is added to them with an electrical jolt so that it
can seek out and break into the BCL11A gene, the one that
controls production of fetal hemoglobin. Then the edited cells are then dripped
back into a blood vessel. They multiply and start making fetal hemoglobin—just
like in those newborns Watson noticed weren’t sick.
It’s all doable—but it’s also a strenuous undertaking for
patients. A bone marrow transplant involves chemotherapy. Doctors have to
destroy your blood system to make room for the edited stem cells. Patients will
spend many weeks in the hospital and can
become infertile from the treatment. Only people with the
most unbearable symptoms—perhaps one in 10 sickle-cell sufferers—are expected
to opt for this cure.
The Vertex treatment is a landmark because we are now in the
era of commercial rewriting of human genomes. “It’s a huge milestone in the
history of humankind and an important stepping-stone to what will be possible
in the future,” says William Pao, a former head of drug development at Pfizer,
who has studied the Vertex drug for an upcoming book on
what ingredients go into medical breakthroughs.
“Every medicine that ever gets approved has to get to a
sweet spot, which is an intersection of scientific, technical, and clinical
understanding,” says Pao. Such combinations are also why new drugs tend to
arrive in packs. You don’t just get one new antidepressant—suddenly there are
five. “Once you have that amazing insight, everyone rushes in,” says Pao. It’s
also true for sickle-cell. Two other gene-editing treatments are now in trials that
also attempt to increase fetal hemoglobin, one from Editas Medicines and one
from Beam Therapeutics. As well, this month the FDA may also approve a gene
therapy from BlueBird Bio that actually adds a complete new copy of the
hemoglobin gene.
Molecular disease
Pao told me he doesn’t think the stories behind new drugs
are getting enough attention. People like to see movies about how Mark
Zuckerberg stole the idea for Facebook or learn how Jony Ive designed the
iPhone. “But with drugs, the names are hard to pronounce, most people don’t
want to be on medicine, and it happens over decades,” he says. “It’s not an app
you have in your hand.”
For sickle-cell, the journey from cause to cure started in
1910, when a US doctor first observed, though a microscope, that the red blood
cells of a man from the West Indies had a “crescent” or “sickle” shape. The
shape is due to mutated hemoglobin, which makes the cells sticky and less able
to carry oxygen around the body.
The disease gained more fame (particularly in scientific
circles) in 1949, when the chemist Linus Pauling, who would win two Nobels,
measured an atomic charge difference between normal and sickled hemoglobin,
leading him to dub sickle-cell the “first molecular disease” and the beginning
of a new age of "scientific" medicine.
In their search for a cure, researchers kept returning to
Watson’s observation about fetal hemoglobin. They would learn that each of us
makes a little of the fetal version—about 1% of our total hemoglobin, though
the amount can vary from person to person. Such variation let researchers study
its effects in adults, almost as if it were a drug they were taking. By the
1990s, doctors had been following sickle-cell patients long enough to observe
that the more fetal hemoglobin they happened to have, the longer they
lived.
Molecular models showing normal adult hemoglobin (left) and
fetal hemoglobin (right.) Both types have two alpha subunits (shown in red),
but the fetal form has 2 gamma subunits (pink) where the adult form has 2 beta
units (blue).
The problem was how to turn up production of fetal
hemoglobin in adults. It is known that nearly all vertebrate animals express
fetal versions of hemoglobin before birth. Scientists assume it’s an
evolutionary adaptation, a way to get more oxygen out of the placenta. Yet even
though the hemoglobin genes had all been found, and sequenced, by the 1980s
(and the full human genome became available around 2003), researchers still had
no idea what was causing the fetal-to-adult switch.
Gene scan
Then a new genetics technology came to the rescue. After the
Human Genome Project was finished, researchers had started to generate rough
genetic maps for thousands of people. This let them correlate small DNA
differences between people with measurable differences in their bodies: how
tall they were or whether they had certain diseases. The new technique, called
a “genome-wide association,” was a statistical method of asking influential
gene variants to step forward and be counted.
The association technique hasn’t always paid off—but
starting in 2007, the gene searches hit pay dirt for sickle-cell. In one study,
for instance, a team in Italy studied DNA from thousands of Sardinians (some of
whom had beta-thalassemia, another hemoglobin disorder, which is shockingly
common on the island) as well from Americans with sickle-cell. When they
compared each person’s DNA with the amount of fetal hemoglobin each had,
variations kept popping up in one gene: BCL11A.
This gene was far from the hemoglobin sequences—in fact, on
an entirely different chromosome. And until then, it had been mostly known for
its connection to some cancers. It was a complete surprise. “No amount of
sequence-gazing would have told you what to look for,” Orkin says now. But the
blaring signal told them this could be the control mechanism. Orkin likes to
illustrate the impact this clue had with a quote from Marcel Proust: “The only
real voyage of discovery consists not in seeking new landscapes but having new
eyes.”
All eyes were now on BCL11A. And very quickly,
Orkin’s students and trainees showed that it could control fetal hemoglobin. In
fact, it was a transcription factor—a type of gene that controls other genes.
By shutting off BCL11A they were able to rekindle production
of fetal hemoglobin in cells growing in their lab—and later, in 2011, they
showed that mice could be cured of sickle-cell in the same fashion. “What this
meant is if you could do this to a patient, you could cure them,” says Orkin.
However, in humans it wasn’t going to be as simple as
turning the gene off altogether. BCL11A turns out to be an
important gene, and losing it wasn’t ultimately good for mice. One study found
mice lacking it were mostly dead within six months. But then came another lucky
break. Those hits from the Sardinia study? They turned out to cluster in a
special region of the BCL11A gene, called an “erythroid
enhancer,” that was active only during the production of red blood cells.
Think of it as a gas pedal for BCL11A, but one
that is exclusively employed when a stem cell is making red blood cells—a big
job, by the way, since your body makes a few billion each day. “It’s absolutely
cell specific,” says Orkin. And that meant the gas pedal could be messed with:
“We’d gone from the whole genome to one [site] that we could exploit therapeutically.”
Drug target
The switch had mostly been a matter of scientific curiosity.
But now researchers at Harvard, and at a company they’d teamed with, Sangamo
Biosciences, began to define a treatment. They peppered the enhancer with every
possible damaging edit they could—“like a bunch of BBs,” says Bauer, who did
the work at Harvard. Eventually, they found the perfect one: a single
disruptive edit that would lower BCL11A by about 70%, and
consequently allow fetal hemoglobin to increase.
The editing target, a short run of a few DNA letters, never
appears elsewhere in most people’s genomes. That’s important, because once
programmed, CRISPR will cut the matching target sequence every time it
encounters it, whether or not you want it to. Creating unintentional extra
edits is considered hazardous, but Bauer says he’s found only one such “off
target" site, which he estimates will appear in the genomes of about 10%
of African-Americans. But its location isn't in a gene, so accidental edits
there aren't expected to matter. Bauer thinks the risk, whatever it is, is
probably a lot lower than the danger posed by having sickle-cell disease.
Stuart Orkin in the lab at Boston Children's Hospital.
BOSTON CHILDREN'S HOSPITAL
There are signs Orkin’s lab may have found a perfect
edit—one that can’t be easily improved on. His institution, Boston Children’s
Hospital, patented the discoveries, and later CRISPR Therapeutics and Vertex
agreed to pay it for rights to use the edit. They’ll likely contribute
royalties, too, once the treatment goes on sale. Orkin told me he thinks the
companies tried to develop an alternative—a different, nearby edit—but hadn’t
been successful. “They tried to find a better [one] but they couldn’t,” says
Orkin. “We have the whole thing.”
Translating that lucky break into a real-world gene-editing
treatment was the bigger, more complex job. And it was not cheap. According to
Solt DB, a company that analyzes biotech finances, financial reports from
CRISPR Therapeutics indicate that manufacturing the treatment, recruiting
hospitals, trying it on about 90 people in a trial, has taken more than $1
billion so far.
It’s a very large investment into a product. For comparison,
it is more than twice what Tesla spent before fielding its first electric car,
the Roadster. But the return could also be high. After the FDA approves the
treatment, sometime this week, Vertex will announce a price. Already, there is
speculation the treatment could cost $3 million, not even including the
hospital stays.
Orkin is ready to credit the companies for their swift
development of the cure. It took them only about eight years. But he thinks it
helped that they had the perfect edit. “To me, all the discovery was done by
2015. We defined how to do it, and then it was a question of execution,” he
says. “But the companies executed flawlessly, and they don’t all do that.”
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