Newswise — This year marks the 10th anniversary of the development of CRISPR as a genome-editing tool, an achievement that earned Jennifer Dounda and Emmanuelle Charpentier the 2020 Nobel Prize in Chemistry. In the world of developing new medical therapies, 10 years is not a long time, but CRISPR-based therapies have made significant strides. In the first five years, the field focused on refining how CRISPR works in different cell types, improving its efficiency at cutting DNA, and developing CRISPR towards clinical applications for the first time. In the following five years, the discovery and engineering of new CRISPR proteins with different capabilities expanded the CRISPR toolbox and the first CRISPR clinical trials began, yielding sometimes stunning results.
The IGI has been closely tracking the development of new CRISPR-based therapies and the progress of the growing number of clinical trials. Over the past year, trials have started in new disease areas including diabetes and HIV/AIDS. In our annual deep dive into CRISPR clinical trials, we guide you through the current landscape of clinical trials, outcomes, what we hope to learn from each trial, and what is coming next in the world of therapeutic genome editing.
CLINICAL TRIAL BASICS
In the United States, the Food and Drug Administration (FDA) assesses new disease treatments for safety and efficacy through clinical trials on patient volunteers. Early trials (phase 1) evaluate safety and treatment side effects. Later trials (phase 2 and 3) evaluate how effective treatments are and compare new therapies to standard treatments. Sometimes trial phases are combined to expedite testing a treatment.
While the number of CRISPR clinical trials is growing each year, most of the current trials using CRISPR-based treatments are still in early stages. That means that even if the treatments are safe and effective, they’re likely still a few years away from a possible FDA approval and being available to patients in the US.
Before we dive into each treatment area, keep in mind that all current CRISPR clinical trials target specific cells or tissues in individuals without affecting sperm or eggs — that is, no DNA changes are intended to be passed onto future generations.
The development of CRISPR genome editing opens up new possibilities in precision medicine. Current trials are underway in seven treatment areas: blood disorders, cancers, inherited eye disease, diabetes, infectious disease, inflammatory disease, and protein-folding disorders.
BLOOD DISORDERS
DISEASE BACKGROUNDS
Red blood cells use the protein hemoglobin to carry oxygen from the air we breathe to the rest of the body. Variations in a gene that encodes part of the hemoglobin molecule cause two genetic disorders: sickle cell disease (SCD) and beta thalassemia.
In sickle cell disease, red blood cells are misshapen. Their “sickle” or crescent shape blocks blood vessels, slowing or stopping blood flow. This causes sudden, severe pain crises. Complications of SCD include chronic pain, strokes, organ damage, and anemia. In beta thalassemia, patients do not make enough of the hemoglobin protein, leading to fatigue and anemia. In severe cases, patients suffer organ damage, especially to the bones, heart, and liver. SCD and beta thalassemia can both be fatal.
SCD disproportionately affects certain populations. Globally, the highest level of incidence is in sub-Saharan Africa. In the United States, SCD mainly affects Black Americans. While SCD was the first identified genetic disease, it has received poor research funding and individuals with SCD tend to receive poorer care compared to individuals with other genetic diseases, like cystic fibrosis, that are more likely to affect wealthier, White individuals. New research into genomic treatments for SCD are an important step towards equity.
There are some treatments available for SCD and beta thalassemia, but patients often have severe symptoms and complications even with treatment. Patients with more severe cases of either condition need frequent blood transfusions. Bone marrow transplant can be curative; however, this can only be done when a healthy, matching donor can be found. Bone marrow transplant is not an option for most SCD or beta thalassemia patients.
TREATMENT STRATEGIES
The approach taken to treat these blood disorders with CRISPR technology in the most advanced trial doesn’t directly correct the gene variants that cause disease. It uses a clever workaround: instead of restoring healthy adult hemoglobin, the goal is to increase levels of fetal hemoglobin. This is a form of hemoglobin that fetuses make in the womb, but children and adults don’t make. We don’t know yet why humans switch from one form of hemoglobin to the other after birth, but fetal hemoglobin is not affected by the sickle cell mutation and can take the place of defective adult hemoglobin in red blood cells. This treatment can be used for both SCD and beta thalassemia.
In individuals with SCD, symptoms start to show during infancy, after fetal hemoglobin (HbF) levels decrease. The first step of treatment is to harvest a patient’s blood stem cells directly from their blood. Next, scientists edit the genomes of these cells to turn the fetal hemoglobin gene on. Then, chemotherapy eliminates the disease-causing blood stem cells from the patient’s body. Finally, billions of genome-edited stem cells are put back into their bloodstream. These genome-edited blood stem cells are administered by IV. If it works as intended, these cells will take up residence in the bone marrow, creating a new blood stem cell population which will make edited red blood cells that produce fetal hemoglobin.
This treatment approach is called ex vivo genome editing, because the editing occurs outside of the patient’s body. The advantage of ex vivo editing is ensuring that genome-editing tools only come in contact with the right target cells. It also avoids the risk of long-term presence of CRISPR components in the body, like unwanted edits or immune reactions.
Other trials that are just beginning or will begin soon also use an ex vivo approach, but are different on a molecular level. One uses base editing rather than conventional CRISPR, to turn on fetal hemoglobin. Two other trials aim to directly correct the mutation that causes sickle cell disease using CRISPR Cas-9, restoring healthy, adult hemoglobin.
CURRENT CRISPR CLINICAL TRIALS
In the first use of an ex vivo CRISPR-based therapy to treat a genetic disease, researchers treated an individual with beta thalassemia in Germany in 2019. CRISPR Therapeutics and Vertex Pharmaceuticals are running this trial in Europe and Canada. According to company press releases, at least 14 more individuals have since been treated and followed for at least three months, with five followed for over a year. The first individual with SCD was treated with the same therapy in Nashville, Tennessee in 2019. At least six more individuals with SCD have been treated since then and followed for at least three months, with two followed for over a year.
So far, patient volunteers with both conditions have made remarkable recoveries.
- Patients treated for SCD or beta thalassemia show normal to near-normal hemoglobin levels, where at least 30% (SCD) or 40% (beta thalassemia) of hemoglobin is fetal hemoglobin.
- Patients with beta thalassemia are free from needing blood transfusions. Patients with SCD are free from transfusions and disabling pain crises.
- Molecular tests on bone marrow from each of six patients a year or more after treatment show the continued presence of genome-edited cells
- One patient with beta thalassemia experienced serious immune reactions to treatment which have since resolved. No other serious adverse events were observed, and side effects seem to be related to chemotherapy, not the genome-editing treatment.
- Hear directly from Victoria Gray or Jimi Olaghere, who were both treated for sickle cell disease.
CRISPR Therapeutics and Vertex Pharmaceuticals are jointly running these combined phase 1, 2, and 3 trials in the US, Canada, and Europe. In Europe and the US, this treatment has been given special status to fast-track approval.
Three more trials for sickle cell disease will begin shortly. Beam Therapeutics has regulatory approval to move forward with another SCD trial aimed at increasing fetal hemoglobin. Beam uses base editing, a form of CRISPR editing that works without double-stranded DNA breaks and which therefore may be safer than conventional CRISPR.
The other two trials — one from Graphite Bio, and the other from a consortium of researchers from IGI, UCSF, UCLA, and UC Berkeley — will test an alternate approach that would use CRISPR to directly repair the mutation that causes SCD, reverting it to the healthy version. Graphite has begun enrolling patients, and the UC trial will begin recruiting patients later in 2022. The UC consortium trial is the only not-for-profit trial for sickle cell disease.
WHAT TO WATCH FOR
Over the last few years, there has been a burst of research into treatments for blood disorders. Pharma, biotech companies, and academic research institutions are working on conventional and genomic therapies. It’s too soon to say which approaches will be the safest and most effective, but patients are sure to benefit from the renewed research in these disease areas.
The initial results from Victoria Gray, Jimi Olaghere, and other patient volunteers are what genome-editors dream of. If trial data continue to be so positive, the treatment could be approved as soon as 2023.
“Bottom line, the progress of CRISPR/Vertex is a landmark in that it’s likely to generate the first approved CRISPR-based medicine,” says Fyodor Urnov, Ph.D., IGI’s Director of Technology and Translation and a 20-year veteran of the sickle cell field. “That would be an extraordinary moment for us. And it will create a wide road for others in this space — like Beam and the UC Consortium — to rapidly follow suit.”
Long-term follow-up of these and other trial participants is crucial: they will be tracked for years to come to see if the treatment remains effective, and to look for potential long-term side effects which wouldn’t be apparent until further down the line, like cancer from unwanted changes to the DNA. It will be especially interesting to see, for instance, if there are differences in outcomes between patients who receive cells edited with conventional CRISPR versus base editing.
“The main side effects so far have been from the chemotherapy necessary to wipe out the pre-existing bone marrow cells in order for the edited cells to engraft. The chemotherapy is a huge limiting factor for these therapies,” explains Megan Hochstrasser, Ph.D., a CRISPR expert who studied with Jennifer Doudna. “If you have to be in the hospital for weeks because you are getting your bone marrow ablated with chemotherapy, which cripples your immune system, it’s risky, expensive, and time-consuming. That’s a huge barrier to scaling this and making it available widely. It’s a big hurdle that could be overcome if someone finds a way to deliver the treatment directly, without bone marrow ablation.”
Scalability — making enough of a treatment to get it to the many people who need it — will be a major challenge for CRISPR-based treatments for blood disorders, both because of the technical challenges of creating the individualized product and administering the treatment protocol, and the cost. The cost of the current CRISPR-based therapy is in the $1–2 million range, and can only be performed at a small number of medical facilities worldwide, putting it well out of reach of the vast majority of people with SCD or beta thalassemia. Research into in vivo approaches, which could eliminate the need for chemotherapy and decrease the associated risks and expenses, is in early stages, but will be a focus of researchers working to make more widely accessible CRISPR-based therapies for blood disorders in the coming years.
CANCERS
DISEASE BACKGROUND
Cancer refers to diseases that are caused by uncontrolled cell growth. Right now, CRISPR-based therapies are mainly aimed at treating blood cancers like leukemia and lymphoma.
TREATMENT STRATEGY
T cells are a type of white blood cell that have a central role in immune system response. T cells are covered in receptors that recognize other cells as safe or threatening. They patrol the body, killing foreign or dangerous cells, or recruiting other cells to assist. In CAR-T immunotherapy, researchers genetically engineer an individual’s T cells to have a receptor that recognizes their cancer cells, telling the T cells to attack.
The immune system is highly regulated to avoid attacking healthy cells. Some T cell receptors work as “checkpoints” that determine whether an immune response occurs. When a T cell PD-1 receptor comes in contact with a molecule called PD-L1 on another cell, it communicates that it is a “safe” cell and the T cell leaves it alone.
Cancer cells often cloak themselves in these safety signals, tricking the patrolling T cells into ignoring them. Researchers are using CRISPR to edit the PD-1 gene in T cells to stop them from making functional PD-1 receptors so they can’t be tricked by cancer cells. This immunotherapy approach is known as checkpoint inhibition, and it is often used in conjunction with CAR-T engineering to give T cells the greatest possible chance of eliminating cancer.
For these treatments, researchers harvest T cells from a patient’s blood and engineer them in a lab. Then, they put them back into the patient’s bloodstream by IV. Because this treatment relies on ex vivo editing, it is easy to deliver the genome-editing tools to the target cells. CAR-T therapy was approved for use in treating blood cancers in 2017.
CURRENT CRISPR CLINICAL TRIALS
In 2016, an individual with lung cancer became the first person in the world to be treated with a CRISPR-based therapy: this patient was injected with PD-1 edited T cells in a Chinese clinical trial. This and an American clinical trial using CRISPR-based immunotherapies for cancer have been completed. Several other clinical trials using CRISPR-based immunotherapies, mainly to treat blood cancers, are ongoing.
In the Chinese trial, researchers at Sichuan University treated 12 patients with non-small-cell lung cancer with PD-1 edited T cells. This approach did not include CAR-T, as it is not currently an option for lung cancers. Like early stage trials in the US, the main goal was to assess safety and side effects rather than efficacy.
In April 2020, the researchers reported that the treatment was safe to administer and had minor side effects like fever, rash, and fatigue. The intended edit was found with a low efficiency: a median of 6% of T cells/patient before infusion back into the patient. Off-target effects — unintended changes at various places in the genome — also occurred at a low frequency and were mostly in parts of the genome that don’t code for proteins. On-target effects — unintended changes at the target site — were more common (median of 1.69%). 11 out of 12 patient volunteers had edited T cells two months after the infusion, although at low levels. Patients with higher levels of edited cells had less disease progression.
The first CRISPR-based therapy trial in the US combined CAR-T and PD-1 immunotherapy approaches, using CRISPR to edit three genes in total. This phase 1 study, run by the University of Pennsylvania in collaboration with the Parker Institute, was completed in 2020. Like the Chinese trial, the goals were to determine if the treatment was safe and had acceptable side-effects, not to cure patients. Two patient volunteers with advanced white blood cell cancer (myeloma) and one with metastatic bone cancer (sarcoma) were treated. Researchers reported that the treatment was safe to administer and had acceptable side effects. The edited T cells took up residency in the bone marrow and remained at stable levels for the nine months of the study. Biopsies on the patient with bone cancer showed that T cells were able to find and infiltrate tumors. Off-target effects were rarely observed. However, unintended edits at the target site were observed frequently, with 70% of cells showing at least one mutation at or near the target site during the T cell manufacturing process. After infusion and over time in patients, the percentage of cells with mutations decreased.
“A really interesting thing is that the American study did show a percentage of the large genomic rearrangements that people fear,” says Hochstrasser. “But the percentage of cells with these changes actually decreased over time. It seemed like the cells that had those types of mutations were dying or getting out-competed by the other cells. So, it seemed like the cells that you wouldn’t want in the body were not actually sticking around in the body, which was a surprise to me, and very encouraging.”
The therapies in the two trials described above are autologous: cells are taken from each patient, edited, multiplied, and then put back into the same patient. This process is expensive, time-consuming, and few facilities can do it. Sometimes the manufacturing process — which is starting with cells from a sick patient — just doesn’t work, produces low potency cells, or individuals die of their disease while waiting for the manufacturing process to be completed.
In October 2021, CRISPR Therapeutics announced results from their ongoing US-based Phase 1 trial for an allogeneic T cell therapy. Allogeneic therapies are made from cells from a healthy donor. These cells are edited to attack cancer cells and avoid being seen as a threat by the recipient’s immune system, and then multiplied into huge batches which can be given to large numbers of recipients. Allogeneic products reduce cost, time until treatment, and potentially provide more consistently potent cells. Allogeneic therapies are sometimes referred to as “off-the-shelf.”
The press release from CRISPR Therapeutics gave preliminary results for individuals with lymphomas who had been treated and followed for at least four weeks after treatment. Side effects were not severe, and the safety profile was superior to other CAR-T products. In these patients, almost 60% showed a positive response to treatment, with 21% showing no sign of disease for six months after a single treatment. This is similar to approved autologous CAR-T therapies made without CRISPR technology.
Together, these studies indicate that CRISPR-engineered CAR-T therapy may be a promising line of treatment: they appear to be fairly safe, the side effects are tolerable, and the treatment does not tend to induce a strong immune reaction.
WHAT TO WATCH FOR
The FDA has already approved CAR-T therapies and PD-1 pathway inhibitors that don’t use genome editing. In other words, the proof-of-principle work for these therapies has already been done successfully.
The efficiency of editing — meaning, the percentage of cells that actually got edits — was poor in both autologous trials. But these trials were done using technology from 2016, and there have been significant improvements over the last six years. These trials are an important proof of concept about the immediate safety and tolerability of the treatment, but hopefully new trials will show improved editing efficiency.
If researchers get better editing efficiency, will genetic checkpoint inhibition work as well or better than checkpoint-blocking drugs? Will PD-1 editing be as or more effective than antibody treatments that disable PD-1? Future research will have to answer these questions. And while right now CRISPR-based CAR-T does not provide an advantage over conventional CAR-T, CRISPR provides options to develop T cell therapies in ways that are not possible with conventional gene therapy. Researchers are working on CRISPR-editing T cell therapies where genes are added at specific locations in the genome, or using base editing to make changes to multiple genes at once.
The push towards allogeneic, or off-the-shelf, treatments is particularly interesting, given the possibility for quicker and broader access. We will be sure to keep an eye on the development of this and other allogeneic cancer immunotherapy products.
There are two more big areas where CRISPR-based immunotherapies for cancer are heading. The first is targeting solid tumors, with at least three early stage trials going on currently. Solid tumors are a tougher challenge than blood cancers. First, in blood cancers, the cancerous cells are easier for immune cells to reach. In solid tumors, immune cells have to infiltrate a solid mass that isn’t friendly to T cells. Second, scientists are still trying to find ways to send T cells specifically to solid tumors. And finally, when T cell therapy is effective, it kills cancer cells. When a high number of cells are killed at once — from a big tumor, or multiple smaller tumors — the dead cells can cause a dangerous inflammation reaction. We’ll definitely be keeping an eye out for safety and side effect data from the new trials.
“People have been thinking of various ways to boost T cell functionality,” says Alex Marson, M.D., Ph.D., IGI’s Director of Human Health and a Professor of Medicine at UCSF. “CRISPR may be useful for adding or removing genes to make T cells more powerful in solid tumors. We’re looking for ways to enhance the functionality and persistence of T cells, and the safety of this approach.”
The other development to keep an eye out for is moving immunotherapy beyond T cells. “Another thing coming down the road is using different cell types,” says Marson. In addition to allogeneic products from healthy donors, researchers are working on developing natural killer cells and stem cell-derived cells to target cancers.
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For the full, extensive review of CRISPR clinical trials underway in 2022, covering blood disorders cancers, genetic blindness, diabetes, chronic UTI, HIV/AIDS, a rare protein-folding disease, and what to look for next from CRISPR-based therapeutics, please see the complete article from the Innovative Genomics Institute.
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