Taking Genome Editing out of the Lab: Cause for Concern?

By Rebecca Delker, PhD

Genome editing – the controlled introduction of modifications to the genome sequence – has existed for a number of years as a valuable tool to manipulate and study gene function in the lab; however, because of inefficiencies intrinsic to the methods used, the technique has, until now, been limited in scope. The advent of CRISPR/Cas9 genome editing technology, a versatile, efficient and affordable technique, not only revolutionized basic cell biology research but has opened the real possibility of the use of genome editing as a therapy in the clinical setting and as a defense against pests destructive to the environment and human health.


CRISPR – Clustered Regularly Interspaced Short Palindromic Repeats – when teamed up with the nuclease, Cas9, to form CRISPR/Cas9 serves as a primitive immune system for bacteria and archaea, able to tailor a specific response to an invading virus. During viral invasion, fragments of the invader’s foreign genome are incorporated between the CRISPR repeats, forever encoding a memory of the attack in the bacterial genome. Upon future attack by the same virus, these memories can be called upon by transcribing the fragments to RNA, which, through Watson-Crick base-pairing, guide Cas9 to the viral genome, targeting it for destruction by induced double strand breaks (DSBs).


While an amazing and inspiring piece of biology in its own right, the fame of CRISPR/Cas9 did not skyrocket until the discovery that this RNA/nuclease team could be programmed to target specific sequences and induce DSBs in the complex genomes of all species tested. Of course the coolness factor of CRISPR technology does not end with the induction of DSBs but rather the use of these breaks to modify the genome. Taking advantage of a cell’s natural DNA repair machinery, CRISPR-induced breaks can be repaired by re-gluing the broken ends in a manner that results in the insertion or deletion of nucleotides – indels, for short – that disrupt gene function. More interesting for genome editing, though, DSBs can also serve as a portal for the insertion of man-made DNA fragments in a site-specific fashion, allowing the insertion of foreign genes or replacement of faulty genes.


CRISPR/Cas9 is not the first technology developed to precisely edit genomes. The DNA-binding (and cutting) engineered proteins, TALENS and Zinc Finger Nuclease (ZFNs), came into focus first but, compared to the RNA-guided Cas9 nuclease, are just a bit clunky – more complex in design with lower efficiency and less affordable. Even prior to these techniques, the introduction of recombinant DNA technology in the 1970s allowed the introduction of foreign DNA into the genomes of cells and organisms. Mice could be made to glow green using a jellyfish gene before the use of nucleases – just less efficiently. Now, the efficiency of Cas9 and the general ease of use of the technology paired with the decreased costs of genome sequencing enable scientists to edit the genome of just about any species, calling to mind the plots of numerous sci-fi films.


While it is unlikely that we will find ourselves in a GATTACA-like situation anytime soon, the potential for the application of CRISPR genome editing to human genomes has sparked conversation in the scientific literature and popular press. Though genome modification of somatic cells (regulators of body function) is generally accepted as an enhanced version of gene therapy, editing of germline cells (carriers of hereditary information) has garnered more attention because of the inheritance of the engineered modifications by generations to come. Many people, including some scientists, view this as a line that should never be crossed and argue that there is a slippery slope between editing disease-causing mutations and creating designer babies. Attempts by a group at Sun Yat-sen University in China to test the use of CRISPR in human embryos was referred to by many as irresponsible and their paper was rejected from top journals including Nature and Science. It should be noted, however, that this uproar occurred despite the fact that the Chinese scientists were working with non-viable embryos in excess from in vitro fertilization and with approval by the appropriate regulatory organizations.


Modifying human beings is unnatural; and, as such, seems to poke and prod at our sense of morality, eliciting the knee-jerk response of no. But, designer babies aside, how unethical is it to target genes to prevent disease – the ultimate preventative medicine, if you will? It is helpful to address this question in a broader context. All medical interventions – antibiotics, vaccinations, surgeries – are unnatural, but (generally) their ethics are not questioned because of their life-saving capabilities. If we look specifically at reproductive technology, there is precedent for controversial innovation. In the 1970s when the first baby was born by in vitro fertilization (IVF), people were skeptical of scientists making test-tube babies­ in labs. Now, it is a widely accepted technique and more than 5 million babies have been born with IVF.


Moving the fertilization process out of the body allowed for the unique possibility to prevent the transmission of genetic diseases from parent to child. Pre-Implantation Genetic Diagnosis (PGD), the screening of eggs or embryos for genetic mutations, allows for the selection of embryos that are free of disease for implantation. More recently, the UK (although not the US) legalized mitochondrial replacement therapy – a technique that replaces faulty mitochondria of the parental egg with that of a healthy donor either prior to or post fertilization. Referred to in the press as the creation of three-parent babies because genetic material is derived from three sources, this technique aims to prevent the transmission of debilitating mitochondrial diseases from mother to child. To draw clearer parallels to germline editing, mitochondria – energy producing organelles that are the likely descendants of an endosymbiotic relationship between bacteria and eukaryotic cells – contain their own genome. Thus, although mitochondrial replacement is often treated as separate from germline editing because nuclear DNA is left untouched, the genomic content of the offspring is altered. There are, of course, naysayers who don’t think the technique should be used in humans, but largely this is not because of issues of morality; rather, their opposition is rooted in questions of safety.


Germline editing could be the next big development in assisted reproductive technology (ART), but, like mitochondrial replacement and all other experimental therapies, safety is of utmost concern. Most notably, the high efficiency of CRISPR/Cas9 relative to earlier technologies comes at a cost. It has been demonstrated in a number of model systems, including the human embryos targeted by the Chinese group, that in addition to the desired insertion, CRISPR results in off-target mutations that could be potentially dangerous. Further, because our understanding of many genetic diseases is limited, there remains a risk of unintended consequences due to unknown gene-environmental interactions or the interplay of the targeted gene and other patient-specific genomic variants. The voluntary moratorium on clinical applications of germline editing in human embryos suggested by David Baltimore and colleagues is fueled by these unknowns. They stress the importance of initiating conversations between scientists, bioethicists, and government agencies to develop policies to regulate the use of genome editing in the clinical setting. Contrary to suggestions by others (and here), these discussions should not impede the progress of CRISPR research outside of the clinical setting. As a model to follow, a group of UK research organizations have publically stated their support for the continuation of genome editing research in human embryos as approved by the Human Fertilisation and Embryology Authority (HFEA), the regulatory organization that oversees the ethics of such research. Already, a London-based researcher has requested permission to use CRISPR in human embryos not as a therapeutic but to provide insight into early human development.


Much of the ethics of taking genome editing out of the lab is, thus, intertwined with safety. It is unethical to experiment with human lives without taking every precaution to prevent harm and suffering. Genome editing technology is nowhere near the point at which it is safe to attempt germline modifications, although clinical trials are in progress testing the efficacy of ZFN-based editing of adult cells to reduce viral titers in patients with HIV. This is not to say that we will never be able to apply CRISPR editing to germline cells in a responsible and ethical manner, but it is imperative that it be subject to regulations to assure the safety of humans involved, as well as to prevent the misuse of the technology.


This thought process must also be extended to the application of CRISPR to non-human species, especially because it does not typically elicit the same knee-jerk response as editing human progeny. CRISPR has been used to improve the efficiency of so-called gene drives, which guarantee inheritance of inserted genes, in yeast and fruit flies; and they have been proposed for use in the eradication of malaria by targeting the carrier of disease, the Anopheles mosquito. It is becoming increasingly important to consider the morality of our actions with regard to other species, as well as the planet, when developing technologies that benefit humanity. When thinking about the use of CRISPR-based gene drives to manipulate an entire species it is of utmost importance to take into consideration unintended consequences to the ecosystem. Though the popular press has not focused much on these concerns, a handful of scientific publications have begun to address these questions, releasing suggested safety measures.


There is no doubt that CRISPR is a powerful technology and will become more powerful as our understanding of the system improves. As such, it is critical to discuss the social implications of using genome editing as a human therapeutic and an environmental agent. Such discussions have begun with the convention in Napa attended by leading biomedical researchers and will likely continue with similar meetings in the future. This dialogue is necessary to ensure equal access to beneficial genome-editing therapies, to develop safeguards to prevent the misuse of technology, and to make certain that the safety of humans and our planet is held in the highest regard. However, too much of the real estate in today’s press regarding CRISPR technology has been fear-oriented (for example) and we run the risk of fuelling the anti-science mentality that already plagues the nation. Thus, it is equally important to focus on the good CRISPR has done and will continue to do for biological and biomedical research.


We are rapidly entering a time when the genomes of individuals around the world will be sequenced completely, along with many other organisms on the planet; however, this is just the tip of the iceberg of our understanding of the complex translation of this genome into life. For over a decade we have known the complete sequence of the lab mouse, but our understanding of the cellular processes within this mouse is still growing every day. Thus, there is an important distinction to be made between knowing a DNA sequence and understanding it well enough to be able to make meaningful (and safe) modifications. CRISPR genome editing technology, as it is applied in basic biology, is helping us make this leap from knowing to understanding in order to inform the creation of remedies for diseases that impact people, animals and our planet; and it is doing so with unprecedented precision and speed.


We must strike a balance that enables the celebration and use of the technology to advance knowledge, while assuring that the proper regulations are in place to prevent premature use in humans and hasty release into the environment. Or, as CRISPR researcher George Church remarked: “We need to think big, but also think carefully.”