Images via NIH /Flickr; Shutterstock. This article was originally published in June 2018 and has since been updated to reflect the latest developments in CRISPR research.
CRISPR technology offers the promise to cure any human genetic disease with gene editing; which one will be the first?
CRISPR/Cas9 was first used as a gene-editing tool in 2012. In just a few years, the technology has exploded in popularity thanks to its promise of making gene editing faster, cheaper and easier than ever before.
CRISPR is short for clustered regularly interspaced short palindromic repeats. The term makes reference to a series of repetitive patterns found in the DNA of bacteria that form the basis of a primitive immune system, defending them from viral invaders by cutting their DNA.
Using this natural process as a basis, scientists developed a gene-editing tool called CRISPR/Cas that can cut a specific DNA sequence by simply providing it with an RNA template of the target sequence. This allows scientists to add, delete or replace elements within the target DNA sequence.
This system represented a big leap from previous gene-editing technologies, which required designing and making a custom DNA-cutting enzyme for each target sequence rather than simply providing an RNA guide, which is much simpler to synthesize.
CRISPR gene editing has already changed the way scientists do research, allowing a wide range of applications across multiple fields. But the technology could also hold great potential as a treatment for human diseases. In theory, CRISPR could let us edit any genetic mutation at will to cure any disease with a genetic origin. In practice, however, CRISPR is still in the beginning stages of its therapeutic development.
Here is a list of some of the first diseases that scientists are tackling using CRISPR/Cas technology, testing its possibilities and limits as a medical tool.
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Cancer is a complex, multifactorial disease, and a cure remains elusive. There are hundreds of different types of cancer, each with a unique mutation signature. CRISPR technology is a game-changer for cancer research and treatment as it can be used for many things, including screening for cancer drivers, identifying genes and proteins that can be targeted by cancer drugs, cancer diagnostics, and as a treatment.
China has spearheaded the first in-human clinical trials using CRISPR/Cas9 as a cancer treatment. The study tested the use of CRISPR to modify immune T cells extracted from a patient with late-stage lung cancer. The gene-editing technology was used to remove the gene that encodes for a protein called PD-1 that some tumor cells can bind to to block the immune response against cancer. This protein, found on the surface of immune cells, is the target of some cancer drugs termed checkpoint inhibitors.
CRISPR technology has also been applied to improve the efficacy and safety profiles of cancer immunotherapy, such as CAR-T cell and natural killer cell therapies. In the U.S., CRISPR Therapeutics is one of the leading companies in this space, developing off-the-shelf, gene-edited T cell therapies using CRISPR, with two candidates in clinical trials. Earlier this year, the U.S. Food and Drug Administration (FDA) granted Orphan Drug designation to Intellia Therapeutics’ CRISPR/Cas9-gene-edited T cell therapy for acute myeloid leukemia.
Despite these milestones, CRISPR technology still has limitations, including variable efficiency in the genome-editing process and off-target effects. Some experts have recommended that the long-term safety of the approach remain under review. Others have suggested using more precise gene-editing approaches such as base editing.
The blood disorders beta-thalassemia and sickle cell disease, which affect oxygen transport in the blood, are the target of a CRISPR treatment being developed by CRISPR Therapeutics and its partner Vertex Pharmaceuticals.
This exa-cel therapy, which is currently being tested in five clinical trials, consists of harvesting bone marrow stem cells from the patients and using CRISPR technology ex vivo to make them produce fetal hemoglobin. This is a natural form of the oxygen-carrying protein that binds oxygen much better than the conventional adult form. The modified cells are then reinfused into the patient.
In September, exa-cel was granted a rolling review by the U.S. FDA as a potential one-time treatment for sickle cell disease and transfusion-dependent beta-thalassemia. This follows the granting of Regenerative Medicine Advanced Therapy, Fast Track, Orphan Drug and Rare Pediatric Disease designations. If approved, exa-cel will become the first CRISPR therapy to achieve regulatory approval for a genetic disease. Vertex will also submit a biologics licensing application for exa-cel in November and a marketing application to the European Medicines Agency by the end of the year.
Hemophilia is another blood disorder that CRISPR technology could tackle, although development is still at the preclinical stage. In 2020, Intellia Therapeutics and Regeneron Pharmaceuticals teamed up to pursue the development of hemophilia A and B CRISPR/Cas9-based treatments.
Many hereditary forms of blindness are caused by a specific genetic mutation, making it easy to use CRISPR/Cas9 to treat it by targeting and modifying a single gene. In addition, the activity of the immune system is limited in the eye, which can circumvent any problems related to the body rejecting the treatment.
The company Editas Medicine is working on a CRISPR therapy for Leber congenital amaurosis, the most common cause of inherited childhood blindness, for which there is currently no treatment. The treatment aims to use CRISPR to restore the function of light-sensitive cells before losing sight completely by fixing the most common genetic mutation behind the disease.
In 2020, the company started a phase 1/2 trial, which was the first trial to test an in vivo CRISPR treatment; this is when gene editing is performed directly inside the patient’s body rather than on cells extracted from their body. The treatment showed positive safety data in adults, and earlier this year, Editas Medicine dosed the first pediatric patient.
There are several ways CRISPR could help us in the fight against AIDS. One is using CRISPR to cut the viral DNA that the HIV virus inserts within the DNA of immune cells. This approach could be used to attack the virus in its hidden, inactive form, which is what makes it impossible for most therapies to completely get rid of the virus.
In September, the first ever individual with HIV was dosed with a CRISPR-based gene-editing therapy in a phase 1/2 trial led by Excision Biotherapeutics and researchers at the Lewis Katz School of Medicine at Temple University in Philadelphia.
Another approach could make us resistant to HIV infections. Certain individuals are born with a natural resistance to HIV thanks to a mutation in a gene known as CCR5, which encodes for a protein on the surface of immune cells that HIV uses as an entry point to infect the cells. The mutation changes the structure of the protein so that the virus is no longer able to bind to it.
This approach was used in a very controversial case in China in 2018, where human embryos were genetically edited to make them resistant to HIV infections. The experiment caused outrage among the scientific community, with some studies pointing out that the “CRISPR babies” might be at a higher risk of dying younger.
The general consensus seems to be that more research is needed before this approach can be used in humans, especially as recent studies have pointed out this practice can have a high risk of unintended genetic edits in embryos.
Cystic fibrosis is a genetic disease that causes severe respiratory problems. Although there are treatments available to deal with the symptoms, the life expectancy is only around 40 years. Cystic fibrosis can be caused by multiple different mutations in the target gene CFTR – over 700 of which have been identified – making it difficult to develop a drug for each mutation. With CRISPR technology, mutations that cause cystic fibrosis can be individually edited.
In 2020, researchers in the Netherlands used base editing to repair CFTR mutations in vitro in the cells of people with cystic fibrosis without creating damage elsewhere in their genetic code. In addition, companies such as Vertex Pharmaceuticals and CRISPR Therapeutics have plans to develop treatments for cystic fibrosis using CRISPR systems. However, these therapies still remain in the research phase.
Duchenne’s muscular dystrophy is caused by mutations in the DMD gene, which encodes for a protein necessary for the contraction of muscles. Children born with this disease suffer progressive muscle degeneration, and existing treatments are limited to a fraction of patients with the condition.
Research in mice has shown CRISPR technology could be used to fix the multiple genetic mutations behind the disease. In 2018, a group of researchers in the U.S. used CRISPR to cut at 12 strategic mutation hotspots covering the majority of the estimated 3,000 different mutations that cause this muscular disease. A company called Exonics Therapeutics was spun out to further develop this approach. A year later, it was acquired by Vertex Pharmaceuticals for approximately $1 billion to accelerate drug development for this disorder.
In July, the U.S. FDA granted permission for one patient to receive a tailor-made CRISPR-based gene therapy for their particular mutation — this mutation is so rare that the therapy will likely only be used once. The Boston non-profit Cure Rare Disease will initiate the clinical trial later this year, which will mark several milestones, including the first ever personalized CRISPR therapy and the first clinical trial to implement any form of gene editing for muscular dystrophy treatment.
Huntington’s disease is a neurodegenerative condition with a strong genetic component. The disease is caused by an abnormal repetition of a certain DNA sequence within the huntingtin gene. The higher the number of copies, the earlier the disease will manifest itself.
Treating Huntington’s could be tricky, as any off-target effects of CRISPR in the brain could have very dangerous consequences. To reduce the risk, scientists are looking at ways to tweak the genome-editing tool to make it safer.
In 2018, researchers at the Children’s Hospital of Philadelphia revealed a version of CRISPR/Cas9 that includes a self-destruct button. A group of Polish researchers opted instead for pairing CRISPR/Cas9 with an enzyme called nickase to make the gene editing more precise.
More recently, researchers at the University of Illinois Urbana-Champaign used CRISPR/Cas13, instead of Cas9, to target and cut mRNA that codes for the mutant proteins responsible for Huntington’s disease. This technique silences mutant genes while avoiding changes to the cell’s DNA, thereby minimizing permanent off-target mutations because RNA molecules are transient and degrade after a few hours.
In the face of the COVID-19 pandemic, CRISPR has quickly been put to use for fast screening tests. In the long term, the gene-editing tool might allow us to fight COVID-19 and other viral infections.
For instance, scientists at Stanford University have developed a method to program a version of the gene-editing technology known as CRISPR/Cas13a to cut and destroy the genetic material of the virus behind COVID-19 to stop it from infecting lung cells. This approach, termed PAC-MAN, was shown to reduce the amount of virus in solution by more than 90 percent.
Another research group at the Georgia Institute of Technology has used a similar approach to destroy the virus before it enters the cell. The method was tested in live animals, improving the symptoms of hamsters infected with COVID-19. The treatment also worked on mice infected with influenza, and the researchers believe it could be effective against 99 percent of all existing influenza strains.
The future of CRISPR technology
Considering that CRISPR/Cas9 is a relatively new development in the world of biology, research has only begun to scratch the surface of the role it could play in the future. The examples listed here are just the first attempts at using CRISPR technology as a therapy. As they progress, we can expect more and more indications to be added to the list.
One of the biggest challenges to turn this research into real cures is the many unknowns regarding the potential risks of CRISPR therapy. Some scientists are concerned about possible off-target effects as well as immune reactions to the gene-editing tool. But as research progresses, scientists are proposing and testing a wide range of approaches to tweak and improve CRISPR in order to increase its efficacy and safety.
Hopes are high that CRISPR/Cas9 technology will soon provide a way to target and destroy complex diseases such as cancer and AIDS, and even target genes associated with mental illnesses.