Relying on an ultra-rare variant, David Liu unveils a new approach to editing sickle cell
There are now at least five different approaches to curing sickle cell in or nearing human testing from at least eight different companies or academic centers. But researchers have not stopped looking for improvements.
David Liu, the co-inventor of base editing and co-founder of Beam Therapeutics, unveiled in Nature Tuesday a new approach for using gene editing to turn patients’ sickling hemoglobin into a healthy form of the protein. If it plays out in humans, experts say, the strategy could offer a more direct and potentially safer way of treating the debilitating genetic disease.
“It’s a step forward,” said Stefano Rivella, who works on gene-based cures for blood disorders at Children’s Hospital of Philadelphia and was not involved in the study. “It’s very promising and definitely something novel compared to the other technologies.”
Over the last half-decade, companies have largely relied on two gene-based strategies for treating sickle cell, neither of which actually deal with the mutation directly. Bluebird bio uses gene therapy to give patients a functioning, lab-synthesized copy of the gene. And the various CRISPR companies — CRISPR Therapeutics, Editas and Intellia — all use a creative workaround: They shatter a gene that stops people from making fetal hemoglobin, the form of the protein that most people stop making in infancy. In sickle cell patients who receive the treatment, the fetal hemoglobin turns back on and begins ferrying oxygen around the body.
Both approaches have yielded functional cures in the clinic, clearing dozens of patients of the devastating pain crises that are the hallmark of the disease. But they also come with risks that, while not yet seen in humans, have been well established in the lab.
To deliver its gene, bluebird relies on lentivirus, a re-engineered form of HIV that integrates randomly into a patients’ DNA and could interfere with genes that suppress tumors. CRISPR breaks the DNA in half, raising similar concerns about how the fracture could reverberate across the genome.
“I’m definitely concerned,” said Hans-Peter Kiem, a gene editing researcher at Fred Hutch. “It’s a theoretical risk, but I’m definitely concerned.”
Despite clinical success, those concerns have only grown in the last couple of years, as researchers spotlighted new ways CRISPR cuts could theoretically mangle the genome: rearranging chromosomes, for example, or interacting in previously unforeseen ways with particular genetic variants common in people with African ancestry.
“We have not seen anything yet (in the clinic),” said Fyodor Urnov, a gene editing researcher at UC-Berkeley. “But this is the classic example of where absence of evidence is not evidence of absence.”
Liu and a postdoc, Greg Newby, tried to find a way to fix the mutation more directly, without breaking anything. That’s not a straightforward task. Sickle cell is caused by a change at a single base: a switch from A to T. Base editing, the strategy Liu pioneered in 2016, allows researchers to swap one base for another without breaking the double-helix, but it only works for a fraction of combinations. T-A isn’t one of them.
Instead, Liu and Newby designed a base editor that would turn the T into a C, mimicking an ultra-rare hemoglobin variant first identified in Makassar, Indonesia. Despite the mutation, people make functional hemoglobin and live healthy lives.
“It’s simply a simpler and more direct way,” Liu said. They’re “converting a gene variant that causes the disease to one that we know exists in people who are healthy.”
Working with Mitchell Weiss’ lab at St. Jude, Liu and Winters used an electric current to get editor into stem cells from human donors, successfully correcting 80% of them. They did the same with mice — removing, editing and transplanting stem cells back into mice, where they persisted and were functional for 16 weeks. They then took stem cells from those mice and transplanted them into new mice — a way of proving that the edited cells had truly supplanted them. Even the mice who had undergone “secondary transplantation” produced 70% edited hemoglobin.
The approach is highly similar to one Beam Therapeutics unveiled in late April, when the company showed data on editing the Makassar mutation into cell lines. Beam CSO Giuseppe Ciaramella said they would take their own approach into the clinic, but that Liu’s provided a proof-of-concept in animals.
“It demonstrates that this Makassar protein is like the normal and functionally cures the disease,” he said.
Ciaramella said Beam planned to develop both the Makassar approach and their own base-edited fetal hemoglobin approach and, after early studies, decide which one to bring into a pivotal trial. The fetal hemoglobin strategy, called Beam-101, should enter the clinic this year, he said, with the Makassar not far behind.
The hope is that the Makassar can provide more benefits than just safety. Ciaramella noted that although fetal hemoglobin has been proven to effectively eliminate patients’ pain crises, many of the disease’s worst effects – including life expectancy in the mid-40s — come not from crises, but from organ damage that builds up over time.
Patients who receive gene editing therapy to producing fetal hemoglobin continue to also produce sickling hemoglobin. It’s possible that eliminating sickling hemoglobin — or at least as much sickling hemoglobin as possible — could further reduce the risk of damage.
“The data for elevating fetal hemoglobin look very impressive, but they’re recent,” said Urnov, who is also developing a CRISPR-based strategy for directly correcting hemoglobin. “The gene therapy data look very impressive. They’re also very recent.”
Urnov added that companies and the medical world had an obligation to bring as many options forward as possible for sickle cell, a disease that primarily affects African Americans and where patients have long been ignored by drug developers and faced systemic discrimination when trying to seek treatment.
Liu’s strategy, though, doesn’t solve all the problems with the first generation of sickle cell gene therapies. Rivella noted that, while their strategy reduces off-target edits, it doesn’t eliminate them entirely.
It also doesn’t get at the biggest risk that’s already shown itself in humans: The intensive conditioning that patients in every trial have to go through before receiving their edited cells. The chemotherapy used, busulfan, has been linked in the past to cancers and experts now suspect it may also have helped trigger the cases of leukemia and myelodysplastic syndrome bluebird recently saw in its sickle cell trials.
Kiem said he could envision using Liu’s strategy with the in-vivo approach he is trying to develop, which would eliminate the need for any kind of conditioning. And other companies are trying to develop gentler alternatives busulfan. The efforts, though, remain early stage.
“As long as people use busulfan,” Rivella said. “It doesn’t matter if you use gene addition, gene editing, or base editing. The problem will be there.”