Why genome editing technologies are creating buzz in medicine

Why genome editing technologies are creating buzz in medicine

Technologies that allow genomic alteration are gaining in popularity, but they will need to overcome key hurdles to become mainstream.

In brief

  • Biotech and pharmaceutical companies have developed several genome editing approaches, but one in particular stands out for its simplicity.
  • Most clinical trials focus on “ex vivo” programs designed for immune-oncology therapies.
  • Scaling and delivery capacity issues remain key challenges in turning these therapies into mainstream medicine.

In the last decade, genome editing technologies have developed at a fast pace in a multitude of diverse fields ranging from basic research to more advanced applications in synthetic biology, biotechnology and biomedicine. According to one market research firm, the genome-editing market will grow at an annual rate of 17% from 2020 to 2025 and reach US$11.2 billion by 2025.1

Genome editing programs have been slowly trickling into the clinic since the mid-2000s. In 2014, clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins were just research tools stirring up excitement in academic labs. Their medical potential was clear, but somewhat distant in terms of a vision of translation into actual treatments. Six years and a Nobel Prize later, the technology is used in more than 20 clinical trials.2 CRISPR’s unique RNA-guided property simplifies the gene editing process and makes the system dynamic, robust and versatile.

However, the rapid development of genome editing technologies and their entry into clinical trials raise the question of scalable manufacturing and delivery to bring these innovations to patients safely and cost effectively.


Chapter 1

What genome editing technologies do

Established and new editing technologies are aiming to edit our genes.

Genome editing technology modifies genetic material ranging from individual cells to entire organisms by adding, deleting or changing a portion of the material. To work, it requires the “ex vivo” (outside of the patient’s body, e.g. into the patient’s cells) or “in vivo” (inside of the patient’s body) delivery of the editing machine.

Genome editing technologies applications include: gene therapy and genetic engineering, which for example correct defective genes in monogenic genetic diseases; cell line engineering, which generates new cell lines for fundamental or applied research through either gain or loss of function; diagnostics that can recognize specific sequences, which can be used to develop molecular diagnostic solutions; and drug discovery and development, from target identification to disease modeling. In this document, we focus on two main technologies that are used in genome editing: Protein based nuclease systems, and RNA-protein based systems.

While several genome editing approaches are in clinical trials, CRISPR is getting gold-standard treatment

Biotech and pharmaceutical companies have developed several genome editing approaches, with most relying on nucleases to alter the genomes in a targeted manner. The four major systems now in use that allow targeted genome editing are:

  • TALENs (transcription activator-like effector nucleases) are fusion proteins that use bacteria-derived DNA binding domains. The DNA recognition site can be up to 40 base pairs long. TALENs are large molecules that are complex to deliver in vivo.
  • ZFNs (zinc finger nucleases) are fusion proteins comprising DNA-binding domains that recognize three- to four-base-pair-long sequences (zinc finger domains). For example, specificity for a 12-base-pair target sequence would require four ZFN domains. ZFNs are easier to deliver in vivo than TALENs, but TALENs are easier to engineer.
  • Meganucleases are endonucleases with a large recognition site (12 to 40 base pairs). They can be engineered to recognize a site of interest, but it can currently take up to 100 days to engineer a meganuclease, while one day is sufficient to make CRISPR target a gene.
  • CRISPR-Cas systems are programmable genome editing systems originally derived from the bacterial immune system. This technology uses a guide RNA (gRNA) to specify the target and lead the nuclease module Cas. As a result, CRISPR-Cas systems are based on RNA-DNA binding instead of protein-DNA recognition. Cas9 is the original nuclease on which the CRISPR system was built. Since then, new Cas proteins have been added to the CRISPR toolbox. Some are smaller, others are less immunogenic, while still others have been engineered to carry other functions, such as recombinases and transposases — non-nuclease-based technologies that depend on mechanisms of genome recombination and reshuffling.

Although other gene editing systems would require the engineering of as many unique TALENs, ZFNs or meganucleases as there are unique targets, CRISPR technology simply requires the design of specific guide RNAs for each target, which are much simpler to create than engineered proteins.

CRISPR’s simplicity and versatility explain its popularity

Despite being the most recent technology, CRISPR dominates the genome editing clinical trials landscape: 27 of 47 trials (57%) rely on this technology. The simplicity and cost effectiveness of CRISPR technology, as well as the ability to multiplex, or edit multiple targets in one setting, can help explain its relative popularity. We expect that the technology will continue to lead the field in the near future.

The high fragmentation of the clinical trial sponsors — 18 sponsors for 25 trials — also reflects CRISPR’s popularity. Sponsors include academic institutions, biotechs and large pharmaceutical companies. In contrast, TALENs, ZFNs and meganucleases are championed by only a handful of companies.


Chapter 2

How genome editing technology is used

Genome editing is moving to clinics, bringing new curative options to many therapy areas.

Most clinical trials (87%) are based on ex vivo programs in which cells are harvested from patients, engineered and then re-infused into the patients. In vivo programs, in which the technologies are the therapeutic themselves, are still complex and present significant challenges, and are therefore currently not a popular choice yet.

Clinical trials assessing gene editing-based therapeutics

Unlike in vivo approaches, in ex vivo approaches, genome editing technologies are an enabler to design new therapeutics. It is easier to edit genes ex vivo in a laboratory and the risk of off-target editing is very limited, largely because cells can be screened for undesirable edits before being transferred into patients. Today, ex vivo applications are limited to specific pathologies, such as malignancies that, like lymphoma or myeloma, are liquid, and rare hematologic diseases, such as sickle cell diseases and beta-thalassemia.

Aside from the technical aspects, the driving factor behind the popularity of ex vivo approaches has been the rise of immuno-oncology. Nearly two-thirds (64%) of ex vivo trials involve CAR-T cells (chimeric antigen receptor T-cells, a type of cell-based therapy). The next largest group of trials are on therapies that involve the engineering of hematopoietic stem cells to treat rare hematological, monogenic diseases.

Meanwhile, allogeneic cell therapies, which are easier to mass manufacture than autologous therapies, have slightly overtaken personalized autologous cell therapies in the pipeline (51% vs. 49% of  trials),3 despite a higher risk of adverse immune responses. Allogeneic genome-edited cells have the potential to provide off-the-shelf products that can overcome the logistical and manufacturing hurdles associated with the production of individualized cell therapies, as well as the limitations associated with autologous systems (e.g. cost, cell scarcity, product variability, donor cell dysfunction).

However, allogeneic approaches must add a level of genome-engineering complexity to prevent immune recognition and rejection. This can be achieved by disrupting the expression of specific surface receptors, which can be done by genome editors. That said, the rise of CAR-NK cells (chimeric antigen receptor NK cells, a type of cell-based therapy using natural killer or NK cells), which have a great promise as a novel cellular immunotherapy platform against cancer and have a potential for generating off-the-shelf products, may mitigate the future need for additional genome editing to reduce the risk of graft-versus-host disease. One biotech company that uses the MAD7 CRISPR system for editing induced pluripotent stem cells (iPSCs) is currently testing an off-the-shelf adoptive NK cell immunotherapy product in acute myeloid leukemia (FT538).4

Currently, CRISPR applications in clinical trials are limited to targeted deletion of DNA. For example, a US biotech uses the technology to delete an intronic portion of the CEP290 gene in patients with Leber congenital amaurosis (LCA10), an ophthalmologic rare disease. The CRISPR system is administered through subretinal injection of adeno-associated viruses (AAVs) carrying a fragment of genetic material coding for both the Cas nuclease and guide RNA. By injecting the vector directly into the eye, the risks of systemic immune response and off-tissue editing are lower.

Another US biotech company administers its candidate systematically through intravenous injection to knock down the transthyretin gene in vivo to cure transthyretin amyloidosis, a neurological disease. To deliver CRISPR, the biotech company has developed a proprietary non-viral platform that uses lipid nanoparticles (LNPs) designed to deliver an mRNA fragment coding for the CRISPR system (Cas nuclease and guide RNA) to the liver.

Compared to AAVs, LNPs are less limited in the amount of nucleic acids that can be delivered per particle, which may prove useful for future applications based on complex edits. This technology is already used in other applications, such as the delivery of mRNA-based vaccines.


Chapter 3

Why key hurdles limit widespread use of genome editing therapies

Scalability and capacity are still limiting factors.

Although biotech and pharmaceutical companies are racing to develop genome editing technologies and many have made it to the clinical trial stage, key hurdles to bring these innovations safely and at reasonable cost to the patients remain, such as scalable manufacturing and drug delivery.

The personalization challenge for scalability of genome editing technologies

Overall, scaling-up genome editing-based cell therapies poses the same challenges as other ex vivo cell therapies. These challenges will differ depending on whether the therapies are autologous or allogeneic.

Personalization poses the most significant challenge for autologous therapies because it introduces variability, both qualitatively and quantitatively, to the process (e.g., number of cells harvested from each patient). This has two implications:

  1. It makes the process complex to scale and requires developing flexible cell culture platforms that manage the heterogeneity in the type and number of cells harvested from the patients.
  2. It implies that multiple platforms would have to be run in parallel through a scale-out rather than a scale-up approach. Some contract development and manufacturing organizations (CDMOs) have already positioned themselves in this space.

Allogenic cell therapies also encounter several pain points related to scalability. However, they are more aligned to traditional biologics, such as scaling up batch sizes. Scaling up the volume of production may prove challenging and be limited by the availability of appropriate reagents, materials and equipment.

For instance, some raw materials — such as cell culture media or growth factors — may not be available at current good manufacturing practice (cGMP) grades or in sufficient volumes. To better understand the manufacturing requirements, partnerships among biotechs, pharmaceutical companies and CDMOs may prove essential. In addition, establishing collaborations as early as the research/development stage may give CDMOs the opportunity to distinguish themselves as privileged relevant partners throughout the product life cycle.

Another challenge, whether autologous or allogeneic, is the transition from manual processes to commercially automated manufacturing, in which the whole process needs to be uniform and regulation compliant. This requires extensive monitoring and control. Developing sensors, software and computer systems that optimize and collect data throughout the product life cycle could help drug developers and manufacturers comply with regulations, while simultaneously accelerating automation and leveraging the collected data for better therapeutic outcomes for patients.

Capacity shortages are challenging for drug delivery technologies

A large issue still plaguing most cell and gene therapies is the worldwide shortage of production capacity for viral vectors. It is estimated that the shortage in cell and gene therapy capacity amounts to more than 500%.5 To overcome this, CDMOs are investing heavily in expansion. In the meantime, however, the gap remains.

To address the shortage, some drug developers are buying manufacturing slots with CDMOs years in advance. Others are investing in their own manufacturing capabilities. Yet, these solutions may prove hard to implement for small biotechs with limited pipelines and little visibility of their future needs.

That is where lipid nanoparticles come into play. These may represent a good alternative to traditional viral vectors, as their capacity to carry nucleic acids is larger than AAVs and their manufacturing does not depend on mammalian cell culture for production. The first siRNA-based therapy and the current mRNA COVID-19 vaccines use an LNP formulation.6

Using LNP as a systemic delivery mode for genome editing technologies may be limited by off-target considerations (delivery to the wrong tissue). Nevertheless, the rise of mRNA therapies, such as the mRNA COVID-19 vaccines, may accelerate the further development and improvement of LNP formulations and could make them even more versatile.


Chapter 4

Why collaboration may be the best way to accelerate speed-to-market

How partnerships can speed up the delivery of new medicines by combining the best of all involved parties.

The buzz around CRISPR is creating an exciting clinical trial landscape and speaks to the larger dynamism of the field. The first approved genome editing therapeutics will set the scene for therapies to come.

Still, hurdles remain to bring these therapies to the market. To overcome them, the different stakeholders may need to consider new ways of working together. They will also need to develop the infrastructure and value chain to support, manufacture and deliver these therapeutics to patients. This leaves plenty of room for further improvements, technologies and opportunities along the whole value chain of new therapies, from the research phase to the development phase, up until commercialization.

As the field continues to develop, new needs and chances are expected to emerge that will ultimately benefit the entire ecosystem and patients.

This article has been authored by Dr. Isabelle Heiber, Dr. Elias Eckert, Dr. Smail Messaoudi and Joey Wilson, all of EY-Parthenon.

The views expressed by the authors are not necessarily those of EY-Parthenon or other members of the global EY organization.


Technologies that enable genomic alteration, at the cell or organism levels have huge upside potential in medicine if they can overcome some key challenges.