The genome-editing decade

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Although still in its early days, this decade is shaping up to be a golden age for genome editing. In 2020, the Nobel Prize in Chemistry was awarded to Emmanuelle Charpentier and Jennifer Doudna for their 2012 demonstration that the bacterial clustered regularly interspaced short palindromic repeats (CRISPR)-Cas defense system could be turned into a genome-editing tool based on RNA-programmable DNA nucleases.¹ The ability to re-direct CRISPR-Cas to a specific DNA target simply by designing a guide RNA catalyzed an explosion of research that has covered the spectrum from fundamental discoveries in biology to the first-in-human clinical trials.

Reflecting on this rapid development, the reviews in this special issue of Molecular Therapy highlight the expansion of genome-editing technologies in recent years. In addition to CRISPR-Cas nucleases, the genome-editing toolbox also includes meganucleases, zinc-finger nucleases, and transcription activator-like effector nucleases (TALENs), and iterations have moved beyond nuclease activities to strategies such as base editing, which can alter sequences without incurring double-stranded DNA breaks, and CRISPR interference (CRISPRi), which can modulate gene expression. We will learn about the pros and cons of the various editing platforms and why the CRISPR-Cas technology was considered by the Nobel Committee as “gene technology's sharpest tool.” It is precision medicine in its truest sense.

There has been a tremendous growth in preclinical gene therapy applications since 2012 (reaching nearly 1,800 this year), with an increasing number of CRISPR-Cas-based genome-editing preclinical therapies. Although only a few applications have so far made it to clinical trials, the field is poised to take advantage of this extensive preclinical pipeline that is targeting some of the most intractable medical conditions. The reviews presented in this issue highlight both the history and the future potential of genome-editing as it continues its explosive growth.

Rosanwo and Bauer (page 3163) discuss how different genome-editing technologies are being applied to hemoglobinopathies such as beta-thalassemia and sickle cell disease (SCD). They provide a comprehensive overview of the different approaches to correcting the sickle cell mutation or restoring beta-globin function in beta-thalassemia, including the reactivation of fetal hemoglobin. SCD is also the disease for which hematopoietic stem cell (HSC) editing with CRISPR-Cas has been used for the first time in patients.² As befits the applications that are pioneering the field, they also discuss current challenges of therapeutic genome editing, especially for patients with hemoglobinopathies, and how this therapy could be simplified and made more accessible to patients. Another important factor discussed is the burden for patients undergoing current ex vivo gene therapy or editing and potential toxicities compared with allogeneic transplantation and how this affects the quality of life for patients.

Rees et al. (page 3125) provide an in-depth review of the development of next-generation CRISPR-Cas technologies founded on base and prime editors.³ They set the scene by including a comprehensive review of the unintended and off-target consequences that can occur with current genome-editing tools and highlight the differences between technologies that require a double-stranded DNA break and those that can instead modify bases without this intermediate step. Current genome-editing clinical studies are reviewed, and aspects of clinical development are discussed, such as regulatory oversight and manufacturing considerations. They conclude by reflecting on access and equity as they relate to the development of preclinical and clinical applications.

Newby and Liu (page 3107) provide a brief summary of the different editing platforms and discuss considerations for the delivery of these technologies. Currently, for all HSC and T cell-editing applications in clinical trials and, still for most preclinical studies, editing is done ex vivo in specialized facilities such as those where bone marrow transplants are performed. This of course limits access to these powerful tools. Newby and Liu discuss progress in applications based on in vivo delivery that target the liver, heart, CNS, eye, ear, and blood cells. They also discuss future prospects for next-generation technologies such as base and prime editors and conclude with promising recent developments in base editor variants that have now been developed with minimized guide-dependent and -independent off-target activity.

Rogers and Cannon (page 3192) survey the emerging field of B cell editing. Monoclonal antibodies are used in many clinical applications, from cancer to infectious disease to autoimmune diseases. However, the cost and need for repeat infusions suggest that in vivo production from engineered cells could have many applications. Editing the authentic immunoglobulin locus in B cells provides the possibility of long-term secretion of specific antibodies, but in a way that also preserves other B cell functions such as differentiation and expansion in response to antigens. Also discussed is the potential for in vivo delivery of gene-editing reagents to B cells, and the development of off-the-shelf cell products.

Murty and Mackall (see page 3153) provide an overview of T cell editing. T cell engineering has seen the largest growth in cell and gene therapies over the past decade. This is largely due to the introduction of chimeric antigen receptor (CAR) and engineered T cell receptors (TCRs) into T cells for cancer applications. To date, most applications have used lentiviral vectors for the CAR or TCR engineering. Now, these are being combined or replaced with gene-editing enhancements to insert the construct more precisely and to improve efficacy and persistence, for example, by editing checkpoint inhibitors or knocking out endogenous TCRs. In addition, strategies are being used to allow for allogeneic off-the-shelf T cell products.⁴

Maynard et al. (page 3140) discuss the use of large animals for genome-editing applications. While preclinical studies in rodents are helpful to determine feasibility for certain indications, large-animal studies can bridge the gap to the clinic. Special considerations for gene editing that cannot be adequately addressed in small animals are long-term follow-up studies, which are necessary to examine both the stability of the editing and any off-target effects. Specific applications are highlighted that showcase ex vivo modification of cells for HIV, hemoglobinopathies, and CAR T cells, and in vivo delivery of gene therapy and editing tools for muscular dystrophy, hypercholesterolemia, and inherited retinal degeneration. The ability to test specific tissue targeting with in vivo delivery platforms is also discussed.

What will the rest of this decade bring for genome editing? In the very near future, as inspiring stories of success in clinical trials are anticipated, safety and careful long-term evaluation must remain critical foci of the field. Transparency about outcomes and setbacks will promote further innovation, and it is encouraging to see that next-generation technologies continue to fine-tune the editing process, minimizing off-target effects and eliminating the need for double-stranded breaks.

With increasing clinical success, another consideration will be how to ensure access to these therapies. The current reliance on ex vivo editing of autologous cells limits such expansion, and new developments are needed to promote safe in vivo editing or to provide readily available off-the-shelf products to truly democratize these therapies.⁵ Urnov on page 3103 also discusses another dilemma with current approaches - the high cost and barriers to developing highly personalized genetic cures - and advocates for his vision of an “N = 1 CRISPR cures” approach. In addition, although all authorized genome editing to date has been aimed at correcting somatic cells, the “CRISPR babies” controversy in 2018 shows that germline editing is also possible.⁶ Although not supported by most scientists and regulatory authorities, the easy access to gene-editing technology that CRISPR-Cas provides means that continued discussions are urgently needed with stakeholders from across society.⁷

The rest of this decade will provide much to reflect on. Finally, we are happy to report that the response to this special issue was robust indeed, so much so that we have had to divide the issue in two parts, the second of which will appear in January 2022, so stay tuned!