Angled DNA Double Helix
Credit: SERGII IAREMENKO / Getty Images

A little over a decade ago, a paper was published in Science1  that made science fiction a reality. Emmanuel Charpentier, Jennifer Doudna, and colleagues reported that they had identified a means of harnessing an element of a bacterial immune system to carry out genome editing in a way that was far easier and more versatile than previous gene-editing tools.

This system is called CRISPR (short for clustered regularly interspaced palindromic repeats) and has since been developed by academics and commercial companies for use in the treatment of diseases caused by genetic mutations.

The technology allows changes to be made to DNA at positions determined by an RNA guide held within a CRISPR-associated protein called Cas9. Cas9 is a nuclease enzyme that cuts both strands of DNA at the site designated by the RNA guide. The cells then repair the DNA either by pasting together the ends of the double-stranded break with a small change in the sequence at that break or by integrating a new piece of DNA at the site of the cut. Importantly, the 20-base guide RNA sequence can be easily changed meaning that it is relatively simple to redirect Cas9 to a different gene.

This simplicity along with improved efficiency and lower cost has meant that CRISPR-Cas9 has rapidly overtaken earlier gene editing technologies based on zinc finger nucleases and transcription activator-like effector nucleases that also generate double-stranded DNA breaks.

Today, the race is on to be the first with an approved CRISPR therapy, and rapid progress suggests that 2023 will likely be a big year for gene editing in terms of clinical success.

Speaking in March of this year at the third international summit on human genome editing in London, David Liu, a professor at the Broad Institute, Harvard University, and a Howard Hughes Medical Institute investigator, and co-founder of a number of companies specializing in gene editing, said that at that time there were 53 therapeutic gene editing clinical trials listed on Two-thirds of these involve CRISPR nucleases, and more than 200 patients have already been treated with therapies targeting sequences that, when disrupted, offer clinical benefit.

How CRISPR works illustration
Figure 1: How CRISPR works.

CRISPR in the blood

At present, the frontrunner in this race appears to be Exa-cel, a CRISPR-Cas9-based treatment for sickle cell disease (SCD) and transfusion-dependent b-thalassemia (TDT), developed in a collaborative effort between Vertex Pharmaceuticals and CRISPR Therapeutics.

SCD is a good target for treatment with gene editing because the pathophysiology is already well-understood and there is a large unmet clinical need. Indeed, millions of people around the world live with SCD, and about 300,000 babies are born with the condition every year.2

The genetic disease results from a mutation in the b-globin gene (HBB) that encodes a major component of adult hemoglobin. The disease is characterized by red blood cells with a crescent or ‘sickle’ shape and results in poor blood oxygen levels and blood vessel blockages. These cause chronic acute pain syndromes, severe bacterial infections, necrosis, chronic organ injury, and shortened lifespan. Yet patients with sickle cell disease are born healthy and only begin to manifest the disease in infancy as the gene for fetal hemoglobin becomes silenced and it is replaced with adult hemoglobin.

There are currently two strategies for using CRISPR to treat people with SCD. The first aims to increase levels of fetal hemoglobin, which is not affected by the HBB mutation, while the second is designed to directly repair the mutation. Both are carried out using an ex vivo approach whereby stem cells are removed from a patient, edited with CRISPR, and then reinfused.

Exa-cel targets the BCL11A erythroid enhancer, which is known to be associated with the level of fetal hemoglobin3 in patients with SCD and TBT. Editing the gene at this position with CRISPR-Cas9 turns off repression of fetal hemoglobin.

Data presented at the American Society for Hematology Annual meeting in December 2022 showed that 31 patients with SCD had been infused with exa-cel, all of whom were free from painful episodes of circulation blockage known as vaso-occlusive crises (VOCs), with follow-up lasting between 2 and 32 months.4 Prior to treatment, participants reported an average of four VOCs per year. After 3 months, the mean proportion of fetal hemoglobin was more than 20%.

At the same meeting, corresponding data were presented for the first 44 patients with TBT who received exa-cel.5 Of these, 42 stopped red blood cell transfusions after treatment. The median time since last transfusion was 9 months, with 16 patients having gone at least 1 year since their last transfusion. In the 2 years before the study, patients received 36 units of blood per year, on average.

Following these results, Vertex and CRISPR Therapeutics announced the completion of biologics license applications (BLAs) to the U.S. Food and Drug Administration (FDA) for exa-cel for both SCD and TDT. The BLAs include requests for priority review, which, if granted, would shorten the FDA’s review of the application from the standard review timeline of 12 months from the time of submission to eight months. This means that the treatment could be approved by the end of this year.

Just weeks after the BLA announcement, Editas Medicine also reached a big milestone on the journey to the SCD clinical market. The company received orphan drug designation for EDIT-301, an investigational gene editing therapeutic for the treatment of SCD.

EDIT-301 is another ex vivo autologous treatment but differs from exa-cel in that it uses the proprietary AsCas12a nuclease to edit the g-globin gene and increase fetal hemoglobin. It is currently being investigated within the RUBY trial, which plans to dose 20 patients with SCD by the end of this year. The first clinical update is expected by the middle of the year.

Away from the commercial realm, the not-for-profit Innovative Genomics Institute (IGI) is working with the University of California on using CRISPR-Cas9 to directly correct the mutation in the HBB gene and restore regular hemoglobin production. Enrollment in a Phase I/II trial of this method is expected to start later this year.6

Despite the progress and the potential for a “one and done” therapy for SCD and TDT, there are still many bottlenecks to widespread distribution, including the ex vivo nature of cell manipulation and the need for intense ablative chemotherapy to replace the blood system prior to treatment.

In vivo gene editing

Apart from SCD and TDT, several other diseases also look set to be treated with CRISPR-based therapies in the not-too-distant future, and some of these involve inducing gene editing inside the body rather than in cells that have been removed and treated in a laboratory.

One of the leading companies working on in vivo gene editing is Intellia Therapeutics. It has two candidates in early-stage clinical trials.

Of the two, NTLA-2002 is slightly further ahead in the regulatory process, with the Phase II part of its Phase I/II trial already underway outside of the United States. In March, Intellia announced that it had gained investigational new drug (IND) clearance for NTLA-2002, which will enable the company to include patients from the United States in this part of the study.

How NTLA-2001 works illustration
Figure 2: How NTLA-2001 works.

NTLA-2002 targets hereditary angioedema (HAE), a condition that affects around one in 50,000 people worldwide and is associated with severe attacks of painful swelling in the body that can be fatal if swelling occurs in the throat and restricts the airways. The gene-editing therapy uses CRISPR-Cas9 to inactivate the kallikrein B1 gene, which encodes for prekallikrein, the kallikrein precursor protein. Overexpression of this protein leads to dysregulated bradykinin signaling, which in turn causes vascular leakage and ultimately swelling.

Data presented at the American College of Allergy, Asthma & Immunology 2022 Annual Scientific Meeting showed that NTLA-2002, which is delivered to hepatocytes in the liver using a lipid nanoparticle (LNP), reduced plasma kallikrein levels by between 65% and 92%, depending on the dose given, among the 10 patients included in the study.7 The mean reduction in attacks was 89% at the end of the 16-week primary observation period with ongoing data still being collected.

Data for NTLA-2001, which targets transthyretin (ATTR) amyloidosis, has also been promising.8 The condition stems from a misfolded protein called TTR and causes amyloid deposits to accumulate in the heart, resulting in progressive heart failure. So far, 27 patients have been treated across two arms of a study where all patients who received a therapeutic dose experienced near or greater than 90% reduction in serum levels of the misfolded TTR protein.

Ian Karp
Ian Karp
SVP, Investor Relations and Corporate Communications
Intellia Therapeutic

“Over the next one to two years, our goal is to have both of these programs in registration or pivotal trials,” says Ian Karp, Intellia’s senior vice president of investor relations and corporate communications.

Intellia also has three products at the IND enabling stage: NTLA-2003 and NTLA-3001, for alpha-1 antitrypsin deficiency-associated liver and lung disease, respectively, and a product it is developing in partnership with Regeneron for hemophilia B.

Along with the in vivo candidates, Intellia has ex vivo products in the pipeline, one of which, NTLA-6001, is in the IND enabling phase for the treatment of CD30+ lymphomas.

Karp tells Inside Precision Medicine that the company has “always had the goal of being a full-spectrum gene editing company. Intellia also believes that their modular platform technology gives them a rapid and reproducible path to drug discovery.

“Many of the elements that we use can be used for other diseases, so when you choose a new target or a new disease, you’re not having to start from scratch,” he says. This helps to reduce both development time and costs.

Early clinical trials of CRISPR-based therapies, both in vivo and ex vivo, are also underway for chronic urinary tract infections (Locus biosciences), HIV (Excision Biotherapeutics), and several cancers, most commonly leukemia and lymphomas for which CRISPR is used to create healthy donor-derived, allogenic “off-the-shelf” CAR-T cells. Companies with CRISPR cancer treatments in Phase I trials include CRISPR Therapeutics (leukemia and lymphoma), and Caribou Biosciences (non-Hodgkin’s lymphomas) as well as the U.K.’s Great Ormond Street Hospital who have a small Phase I trial using CD19 targeting cells in children with B cell leukemias.

Moving on from double-strand breaks

The gene editing landscape is changing quickly, not only with the number of agents moving into clinical trials, but also in terms of the technology used.

Waseem Qasim
Waseem Qasim
Professor of Cell and Gene Therapy, NIHR senior Investigator, UCL Great Ormond Street Institute of Child Health, London, Consultant In Paediatric Immunology, Great Ormond Street Hospital

“Whatever we’re using now may not be what we use in five or 10 years’ time. It’s moving on,” says Waseem Qasim, professor of cell and gene therapy at the UCL Great Ormond Street Institute of Child Health in London.

Base editing is an example of how things are moving on. Developed by Liu’s lab at Harvard, base editing enables more precise gene correction than does traditional CRISPR.9 Base editors install or correct the four most common types of point mutations at targeted DNA sites without requiring double-stranded breaks or donor DNA templates.

For CRISPR therapies, “clinical trials to date have mostly been limited to diseases such as SCD or ATTR where gene disruption or deletion can be therapeutic rather than the much larger set of indications that could be addressed by precise gene correction,” Liu says.

Qasim’s lab was the first to report Phase I results of a base editing clinical trial, and the findings attracted much media attention. The research team used the technology to create multiplex-edited CAR T cells for pediatric relapsed/refractory T cell acute lymphoblastic leukemia (T-ALL).10 The first patient was treated in May 2022. Bone marrow assessment at 28 days showed morphologic remission, and to date the cancer remains undetected. Two further patients have also been treated, with investigators hoping to recruit 10 in total. Qasim says that a publication with early clinical findings is currently under review.

There are three other Phase I trials of base editing candidates underway: VERVE-101, BEAM-101, and BioRay Laboratories’ BRL-103, targeting familial heart disease, SCD/TDT, and TDT, respectively. Another, BEAM-201, is a multiplexed edited CAR T cell therapy for ALL and acute myeloid leukemia that has cleared IND enabling, and two are in the IND enabling phase for glycogen storage disease and alpha-1 antitrypsin deficiency (BEAM-301 and BEAM-302).

To enable precise gene editing beyond the mutation that can be installed by base editing, Liu and team have also developed prime editing, which uses nicked target DNA to prime reverse transcription of an edited sequence encoded in a prime editing guide RNA (pegRNA). This pegRNA not only specifies the target site for editing but also encodes the edit.

Liu says that prime editors enable highly versatile and precise gene editing that can perform all 12 possible types of DNA substitutions, as well as precise targeted deletions and insertions without the need for double stranded breaks or donor DNA templates. His laboratory is currently looking at whether prime editing could be used to correct the root cause of trinucleotide repeat disorders such as Huntington’s disease and Friedreich’s ataxia.

Limitations of current gene editing technology

Although there have now been several clinical trials showing success with gene editing, others have not yet achieved what they set out to. The CRD-TMH-001 clinical trial, for example, was initiated by biotech nonprofit Cure Rare Disease (CRD) to treat a single person—the brother of the CRD founder—with muscular dystrophy. The participant, Terry Horgan, died some time after the administration of treatment, and the company recently announced that his death was likely due to an adverse reaction to the viral vector used to deliver the experimental therapeutic. Reactions to viral vectors are a common complication, and many companies are now researching newer vectors, such as LNPs, for delivering treatments in vivo.

Despite some clinical success with EDIT-101, a treatment for blindness stemming from Leber congenital amaurosis 10, Editas decided to stop clinical development of the treatment because the clinical population is so small. It may be resumed in the future with an appropriate partner, the company has said. In another setback, Graphite Bio discontinued development of its lead program, the SCD gene therapy nulabeglogene autogedtemcel (nula-cel), following a severe adverse event (pancytopenia) that was deemed likely to be related to the treatment.

Small clinical populations are common for genetic diseases, and the cost and time needed to develop treatments for each of these patients can be prohibitive. To address this, scientists at the IGI are working to improve access to treatments by using a dispensable gene on chromosome 19, in combination with genome editing, as a genomic safe harbor where they can “plug and play” a corrective transgene for individual recessive diseases, explained Fyodor Urnov, a professor of molecular and cell biology at the University of California, Berkeley, and director of technology & translation at the IGI, at the human genome editing summit.

The idea is that “the mutant gene is still there but the disease is recessive, leaving a healthy stem cell which can be transplanted back into the patient,” he said. This platform method could also allow transition from building a treatment for one mutant disease to another at a fraction of the cost of current treatments, since all that needs to change is a single strand of DNA template.

Urnov said that the IGI has set a goal to have this method in the clinic within 3 years, then to move on to the next indication within 6 months. It is aiming for regulatory approval for 12 to 16 “n of 1” diseases in the next 5 to 7 years.

Despite barriers that still need to be overcome, it is clear that recent and future developments in gene editing technology could genuinely change lives.

Summarizing what is ahead, Liu said: “I am hopeful because quite simply, the relentless use of our collective efforts to improve our condition and those of our children is perhaps the defining trait of our species.” Gene editing technologies, he continued, are “the fruits of an ongoing 70-year-old quest to develop one of the most fundamental capabilities of humanity: The ability to have some say in the sequence of our genomes so that we are no longer so beholden to the misspelling in our DNA.”



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  3. Frangoul H, Altshuler D, Capellini Y-S, et al. CRISPR-Cas9 gene editing for sickle cell disease and b-thalassemia. N Engl J Med 2021; 384 252–260
  4. Frangoul H, Locatell F, Bhatia M, et al. Efficacy and Safety of a Single Dose of Exagamglogene Autotemcel for Severe Sickle Cell Disease. Blood 2022;
  5. Locatelli F, Lang P, Li A, et al. Efficacy and Safety of a Single Dose of Exagamglogene Autotemcel for Transfusion-Dependent β-Thalassemia. Blood 2022;
  9. Komor AC, Kim YB, Packer MS, et al. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature 2016; 533: 420–424
  10. Chiesa R, Georgiadis C, Ottaviano G et al. Tvt CAR7: Phase I Clinical Trial of Base-Edited “Universal” CAR7 T Cells for Paediatric Relapsed/Refractory T-ALL. Blood 2022;


Laura Cowen is a freelance medical journalist who has been covering healthcare news for over 10 years. Her main specialties are oncology and diabetes, but she has written about subjects ranging from cardiology to ophthalmology and is particularly interested in infectious diseases and public health.

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