The one huge obstacle standing in the way of progress on gene-editing medicine

The genetic data that underpins CRISPR has a big diversity problem.

Medicine has entered a new era in which scientists have the tools to change human genetics directly, creating the potential to treat or even permanently cure diseases by editing a few strands of troublesome DNA. And CRISPR, the gene-editing technology whose creators won the Nobel Prize for Chemistry in 2020, is the face of this new normal.

CRISPR’s novel harnessing of bacterial proteins to target disease-carrying genes has reshaped medical research over the past decade. While gene-editing itself has been around for more than 30 years, scientists can use CRISPR to edit genomes faster, cheaper, and more precisely than they could with previous gene-editing methods. The method’s novel harnessing of bacterial proteins to target disease-carrying genes has reshaped medical research over the past decade.

As a result, investigators have gained far more control over where a gene gets inserted and when it gets turned on. That in turn has opened the door to a new class of better gene therapies — treatments that modify or replace people’s genes to stop a disease.

Last December, the US Food and Drug Administration approved the first-ever CRISPR-based therapy, designed to treat sickle cell disease. In February, the treatment, called Casgevy, gained approval from the European Commission as well. It joins the dozen or so pre-CRISPR gene therapies that are already available to patients.

But there’s a significant impediment to maximizing CRISPR’s potential for developing novel therapies: the lack of diversity in genetics research.

For decades, gene therapy has been defined by both its enormous therapeutic potential, and by the limitations imposed by our imprecise knowledge of human genetics. Even as gene-editing methods, including CRISPR, have become more sophisticated over the years, the data in the genetic databases and biobanks that scientists use to find and develop new treatments are still riddled with biases that could exclude communities of color from enjoying the full benefits of innovations like CRISPR. Unless that gap is closed, CRISPR’s promise won’t be fully fulfilled.

Developing effective gene therapies depends on growing our knowledge of the human genome. Data on genes and their correlation with disease have already changed the way cancer researchers think about how to design drugs, and which patients to match with which drug.

Scientists have long known that certain genetic mutations that disrupt regular cell functions can cause cancer to develop, and they have tailored drugs to neutralize those mutations. Genetic sequencing technology has sped that progress, allowing researchers to analyze the genetics of tumor samples from cancer patients after they’ve participated in clinical trials to understand why some individuals respond better than others to a drug.

In a clinical trial of the colorectal cancer drug cetuximab, investigators found retrospectively that tumors with a mutation in the KRAS gene (which helps govern cell growth) did not respond to treatment. As a result, clinicians are now asked to confirm that patients do not have the mutation in the KRAS gene before they prescribe that particular drug. New drugs have been developed to target those mutations in the KRAS gene.

It’s a step-by-step process from the discovery of these disease-related genes to the crafting of drugs that neutralize them. With CRISPR now available to them, many researchers believe that they can speed this process up.

The technology is based on — and named after — a unique feature in the bacterial immune system that the organism uses to defend itself against viruses. CRISPR is found naturally in bacteria: It’s short for Clustered Regularly Interspaced Short Palindromic Repeats, and it functions like a mugshot database for bacteria, containing snippets of genetic code from foreign viruses that have tried to invade in the past.

When new infections occur, the bacteria deploys RNA segments that scan for viral DNA that matches the mugshots. Special proteins are then dispatched to chop the virus up and neutralize it.

To develop CRISPR into a biotech platform, this protein-RNA complex was adapted from bacteria and inserted into human and animal cells, where it proved similarly effective at searching for and snipping strands of DNA.

Using CRISPR in humans requires a few adjustments. Scientists have to teach the system to search through human DNA, which means that it will need a different “mugshot database” than what the bacteria originally needed. Critical to harnessing this natural process is artificial RNA, known as a guide RNA. These guide RNAs are designed to match genes found in humans. In theory, these guide RNAs search for and find a specific DNA sequence associated with a specific disease. The special protein attached to the guide RNA then acts like molecular scissors to cut the problematic gene.

CRISPR’s therapeutic potential was evident in the breakthrough sickle cell treatment approved by the FDA late last year. What made sickle cell such an attractive target is not just that it affects around 20 million people or more worldwide, but that it is caused by a mutation in a single gene, which makes it simpler to study than a disease caused by multiple mutations. Sickle cell is one of the most common disorders worldwide that is caused by a mutation in a single gene. It was also the first to be characterized at a genetic level, making it a promising candidate for gene therapy.

In sickle cell disease, a genetic mutation distorts the shape of a person’s hemoglobin, which is the protein that helps red blood cells carry and deliver oxygen from the lungs to tissues throughout the body. For people with sickle cell disease, their red blood cells look like “sickles” instead of the normal discs. As a result, they can get caught in blood vessels, blocking blood flow and causing issues like pain, strokes, infections, and death.

Since the 1990s, clinicians have observed that sickle cell patients with higher levels of fetal hemoglobin tend to live longer. A series of genome-wide association studies from 2008 pointed to the BCL11A gene as a possible target for therapeutics. These association studies establish the relationships between specific genes and diseases, identifying candidates for CRISPR gene editing.

Casgevy’s new CRISPR-derived treatment targets a gene called BCL11A. Inactivating this gene stops the mutated form of hemoglobin from being made and increases the production of normal non-sickled fetal hemoglobin, which people usually stop making after birth.

Out of the 45 patients who have received Casgevy since the start of the trials, 28 of the 29 eligible patients who have stayed on long enough to have their results analyzed reported that they have been free of severe pain crises. Once the treatment moves out of clinical settings, its exact effects can vary. And if the underlying data set doesn’t reflect the diversity of the patient population, the gene therapies derived from them might not work the same for every person.

Sickle cell disease as the first benefactor of CRISPR therapy makes sense because it’s a relatively simple disorder that has been studied for a long time. The genetic mutation causing it was found in 1956. But ironically, the same population that could benefit most from Casgvey may miss out on the full benefits of future breakthrough treatments.

Scientists developing CRISPR treatments depend on what’s known as a reference genome, which is meant to be a composite representation of a “normal” human genome that can be used to identify genes of interest to target for treating a disease.

However, most of the available reference genomes are representative of white Europeans. That’s a problem because not everybody’s DNA is identical: Recent sequencing of African genomes shows that they have 10 percent more DNA than the standard reference genome available to researchers. Researchers have theorized that this is because most modern humans came out of Africa. As populations diverged and reconcentrated, genetic bottlenecks happened, which resulted in a loss of genetic variation compared to the original population.

Most genome-wide association studies are also biased in the same way: They have a lot of data from white people and not a lot from people of color.

So while those studies can help identify genes of importance that could lead to effective treatments for the population whose genes make up the majority of the reference data — i.e., white people — the same treatments may not work as well for other nonwhite populations.

“Broadly, there’s been an issue with human genetics research — there’s been a major under-representation of people of African ancestry, both in the US and elsewhere,” said Sarah Tishkoff, professor of genetics and biology at the University of Pennsylvania. “Without including these diverse populations, we’re missing out on that knowledge that could perhaps result in better therapeutics or better diagnostics.”

Even in the case of the notorious breast cancer gene BRCA1, where a single gene mutation can have a serious clinical impact and is associated with an increased risk of developing cancer, underlying mutations within the gene “tend to differ in people of different ancestries,” Tishkoff said.

These differences, whether large or small, can matter. Although the vast majority of human genomes are the same, a small fraction of the letters making up our genes can differ from person to person and from population to population, with potentially significant medical implications. Sometimes during sequencing, genetic variations of “unknown significance” appear. These variants could be clinically important, but because of the lack of diversity in previous research populations, no one has studied them closely enough to understand their impact.

“If all the research is being done in people of predominantly European ancestry, you’re only going to find those variants,” Tishkoff said.

Those limitations affect scientists up and down the developmental pipeline. For researchers using CRISPR technology in preclinical work, the lack of diversity in the genome databases can make it harder to identify the possible negative effect of such genetic variation on the treatments they’re developing.

Sean Misek, a postdoctoral researcher at the Broad Institute of MIT and Harvard, started developing a project with the goal of investigating the differences in the genetic patterns of tumors from patients of European descent compared to patients of African descent. CRISPR has become a versatile tool. Not only can it be used for treatments, but it can also be used for diagnostics and basic research. He and his colleagues intended to use CRISPR to screen for those differences because it can evaluate the effects of multiple genes at once, as opposed to the traditional method of testing one gene at a time.

“We know individuals of different ancestry groups have different overall clinical responses to cancer treatments,” Misek said. “Individuals of recent African descent, for example, have worse outcomes than individuals of European descent, which is a problem that we were interested in trying to understand more.”

What they encountered instead was a roadblock.

When Misek’s team tried to design CRISPR guides, they found that their guides matched the genomes in the cells of people with European and East Asian ancestry, whose samples made up most of the reference genome, but not on cells from people of South Asian or African ancestry, who are far less represented in databases. In combination with other data biases in cancer research, the guide RNA mismatch has made it more difficult to investigate the tumor biology of non-European patients.

Genetic variations across ancestry groups not only affect whether CRISPR technology works at all, but they can also lead to unforeseen side effects when the tool makes cuts in places outside of the intended genetic target. Such side effects of “off-target” gene edits could theoretically include cancer.

“A big part of developing CRISPR therapy is trying to figure out if there are off-targets. Where? And if they exist, do they matter?” said Daniel Bauer, an attending physician at Dana-Farber/Boston Children’s Cancer and Blood Disorders Center.

To better predict potential off-target edits, Bauer collaborated with Luca Pinello, associate professor at Massachusetts General Hospital and Harvard Medical School, who had helped develop a tool called CRISPRme that makes projections based on personal and population-level variations in genetics. To test it, they examined the guide RNA being used for sickle cell disease treatment, and found an off-target edit almost exclusively present in cells donated by a patient of African ancestry.

It is currently unclear if this off-target edit detected by the CRISPRme tool has any negative consequences. When the FDA approved the sickle-cell therapy in December 2023, regulators required a post-marketing study to look into off-target effects. Any off-target edits affecting a person’s blood should be easily detected in the blood cells, and drawing blood is easier to do than collecting cells from an internal organ, for example.

The genetic variant where the off-target effect occurred can be found in approximately every 1 in 10 people with African ancestry. “The fact that we actually were able to find a donor who carried this variant was kind of luck,” Bauer said. “If the cells we were using were only of European ancestry, it would’ve been even harder to find.”

“Most of these [off-target] effects probably won’t cause any problems,” he said. “But I think we also have these great technologies, so that’s part of our responsibility to look as carefully as we can.”

These issues recur again and again as investigators hunt for novel treatments. Katalin Susztak, professor of medicine and genetics at the University of Pennsylvania, thinks one promising candidate for a future CRISPR therapy is a standout gene for kidney disease: APOL1.

Researchers identified the gene when they looked into kidney disease risk in African Americans. While genome-wide association studies turned up thousands of distinct genes increasing risk for people of European ancestry, in African Americans, this single gene was responsible for “3 to 5 times higher risk of kidney disease in patients,” said Susztak.

The APOL1 variant is common among African Americans because it protects people from developing African sleeping sickness, which is spread by the Tsetse fly present across much of the continent. This is similar to the story of the sickle cell mutation, which can protect people from malaria.

“The variant is maybe only 5,000 years old, so this variant has not arisen in Europe, Asia, or anywhere else. Just in West Africa,” Susztak said. “But because of the slave trades, West Africans were brought to the United States, so millions of people in the United States have this variant.”

The variant also predisposes people to develop cardiovascular disease, high blood pressure, and COVID-related disease, “which maybe explains why there was an increased incidence of deaths in African Americans during COVID than in Europeans,” Susztak said. “APOL1 is potentially a very interesting target [for CRISPR] because the disease association is strong.”

A CRISPR treatment for kidney disease is currently being investigated, but using the tool comes with complications. Cutting the APOL1 gene would set off an immune response, Susztak noted, so they will have to somehow prevent undesirable side effects, or find a related, but editable gene, like they did with sickle cell.

An alternative RNA-based strategy utilizing CRISPR is also in the works. DNA needs to be transcribed into a messenger RNA sequence first before it can be turned into proteins. Instead of permanently altering the genome, RNA editing alters the sequence of RNAs, which can then change what proteins are produced. The effects are less permanent, however, lasting for a few months instead of forever — which can be advantageous for treating temporary medical conditions.

And it may turn out that gene therapy is simply not the right approach to the problem. Sometimes, a more conventional approach still works best. Susztak said that a small molecule drug developed by Vertex — which works similarly to most drugs except special classes like gene therapies or biologics — to inhibit the function of the APOL1 protein has enjoyed positive results in early clinical trials.

Even with these limitations, more CRISPR treatments are coming down the pike.

As of early last year, more than 200 people have been treated with experimental CRISPR therapies for cancers, blood disorders, infections, and more. In the developmental pipeline is a CRISPR-based therapeutic from Intellia Therapeutics that treats transthyretin amyloidosis, a rare condition affecting the function of the heart tissues and nerves. The drug has performed well in early trials and is now recruiting participants for a Phase III study. Another CRISPR drug from Intellia for hereditary angioedema, a condition that causes severe swelling throughout the body, is slated to enter Phase III later this year.

As the CRISPR boom continues, some research groups are slowly improving the diversity of their genetic sources.

The All of Us program from the National Institutes of Health, which aims to find the biological, environmental, and lifestyle factors that contribute to health, has analyzed 245,000 genomes to date, over 40 percent of which came from participants who were not of European ancestry. They found new genetic markers for diabetes that have never been identified before.

Then there’s the Human Pangenome project, which aims to create a reference genome that captures more global diversity. The first draft of its proposal was released last May. Another project called the PAGE study, funded by the National Human Genome Research Institute and the National Institute on Minority Health and Health Disparities, is working to include more ancestrally diverse populations in genome-wide association studies.

But at the current pace, experts predict that it will take years to reach parity in our genetic databases. And the scientific community must also build trust with the communities it’s trying to help. The US has a murky history with medical ethics, especially around race. Take the Tuskegee experiment that charted the progression of syphilis in Black American men while hiding the true purpose of the study from the participants and withholding their ability to seek treatment when it became available, or the controversy over Henrietta Lacks’ cervical cells, which were taken and used in research without her consent. Those are just two prominent historical abuses that have eroded trust between minority communities and the country’s medical system, Tishkoff said. That history has made it more difficult to collect samples from marginalized communities and add them to these critical data sets.

Where the research is being done, where the clinical trials are being held, as well as who’s doing the research, can all have an impact on which patients participate. The Human Genetics & Genomics Workforce Survey Report published by the American Society of Human Genetics in 2022 found that 67 percent of the genomic workforce identified as white. Add in the financial burden of developing new treatments when using a reference genome, or a pre-made biobank from past efforts to collect and organize a large volume of biological samples, saves time and costs. In the race to bring CRISPR treatments to market, those shortcuts offered valuable efficiency to drug makers.

What this means is that the “first-generation” of CRISPR therapeutics might therefore be blunter instruments than they might otherwise be. However, if improvements can be made to make sure the source genomes reflect a wider range of people, Pinello believes that later generations of CRISPR will be more personalized and therefore more effective for more people.

Finding the genes and making drugs that work is, of course, momentous — but ultimately, that’s only half the battle. The other worry physicians like Susztak have is whether patients will be able to afford and access these innovative treatments.

There is still an overwhelming racial disparity in clinical trial enrollment. Studies have found that people of color are more likely to suffer from chronic illness and underuse medications like insulin compared to their white counterparts. Gene therapies easily rack up price tags in the millions, and insurance companies, including the Centers for Medicare and Medicaid Services, are still trying to figure out how to pay for them.

“Because it’s the pharmaceutical industry, if they don’t turn around profit, if they cannot test the drug, or if people are unwilling to take it, then this inequity is going to be worsened,” said Susztak. “We are essentially going to be creating something that makes things worse even though we are trying to help.”