Can gene drives work safely and effectively in populations of genetically diverse, invasive pests?

Background

The world is facing many challenges today, a significant one being the management of non-endigenous pest species. Invasive pest populations can be harmful for biodiversity, food security, and human health. Examples of such invasive species include rats and mice on many islands, rabbits and cane toads in Australia, stoats and possums in New Zealand, and several mosquito species worldwide, among many others. In many cases, the pest species is so widely distributed that conventional management techniques fail to address the scope of the problem. Furthermore, current control methods often cause harmful off-target effects, for example insecticides, or are unethical, such as shooting, poisoning, and trapping. Therefore, we need more effective, species-specific, and ethical methods to control invasive species. Genetic population control is a promising candidate because it potentially ticks all three of these boxes. Examples of genetic population control are sterile insect technology, RNA interference, and most recently, gene drive technology. 

Gene drive is a natural phenomenon whereby a genetic element is inherited at a super-Mendelian rate. There are a range of mechanisms through which gene drive can occur. These mechanisms are harnessed in synthetic gene drives, which enables the rapid spread of a trait through a population. A gene drive can be designed for two ends. First, they can be used for population modification, for example the immunization of a threatened species or vector of disease against a pathogen, or the removal of resistance against pesticides in a pest species. Second, gene drives can be used for population suppression, for example the removal of invasive species, vectors of disease, or agricultural pests. In this case, the gene drive incurs a significant recessive fitness cost to its bearer. 

The potential of gene drives to be used for population suppression has been recognized for over 60 years. However, until the discovery of CRISPR-based genome editing, even if the design would be robust and anticipating constraints in its spread, the technology was hard to engineer. After this break-through, CRISPR-based gene drives were quickly built in yeast, fruit fly, two mosquito species, and mouse. For all organisms except mice, gene drive inheritance is higher than 90%, and often over 99% efficient, meaning that 99% of the offspring of a gene drive carrier inherits the gene drive. Recent cage trials in mosquito have shown that a gene drive becomes fixed in the population after around 10 generations and leads to complete population suppression. Now, researchers are starting to look towards field trials for further testing. 

Most recently, gene drive technology faced challenges in two areas: stability and safety. Regarding stability, resistance alleles have evolved in all organisms in which gene drives were tested. As CRISPR-based gene drives use a roughly 20 base pair long guide-RNA (gRNA) that matches the homologous sequence on the other chromosome, mutations in this target sequence will render de gene drive ineffective. The mechanism through which resistance alleles are formed is facilitated by the gene drive itself: a double stranded break made by cas9 is sometimes repaired through non-homologous end-joining instead of the desired homology directed repair. When non-homologous end joining leads to functional repair of the gene, but with a different sequence, a resistance allele is born. Thus, efficiency and evolutionary stability are inherently linked: the more efficient a gene drive is, the more stable it will likely be. Several strategies have been proposed to prevent or remove resistance alleles: finding more specific germline promotors, targeting extremely conserved sequences so that any resistance allele will likely have a deleterious effect, using multiple gRNAs, and the use of a cleave-and-rescue mechanism. With some careful engineering, it now seems likely that gene drive technology can overcome resistance alleles and remain evolutionarily stable over long periods of time, although this remains to be demonstrated in long-term tests. 

Safety is the second major challenge for gene drive technology, as a gene drive could theoretically spread indefinitely and invade non-target populations. Physical barriers will almost inevitably be insufficient to prevent natural or illegal human-mediated migration. Therefore, a range gene drives have been designed that are less invasive by nature or mitigate risks to an extent. Some stop spreading after a certain number of generations and are thus self-limiting, some require high introduction frequencies, some can stop or remove a gene drive that is already present in a population, and some target locally fixed alleles so that the gene drive will not spread in non-target populations. Cage and field trials are needed to indicate the best trade-off between the power and safety of these self-limiting gene drives and will depend on the organism and its environment.

Project description

Gene drive technology may soon enter the next stage of testing, which will be field trials. However, there are still open questions that are essential to answer for developing field trials in the first place. Currently, most studies are testing gene drives in small cage populations using genetically homogenous lab strains. Therefore, there are still many open questions about the efficiency of gene drive in genetically diverse populations, the evolutionary stability over long periods of time, the practical applicability of safety mechanisms such as gene drives targeting locally fixed alleles, and the influence of real-world population structures on gene drive spread. With these knowledge gaps we cannot form realistic expectations on how field trials might go and in turn if gene drive technology may indeed be a sustainable method of invasive pest control. This could lead to failures or inefficiencies, which in turn might have a negative impact on the public perception of this technology. Therefore, this project aims to guide the development of field trials and public discussion by helping to answer abovementioned open questions on the evolutionary prerequisites for safe and effective gene drive deployment to control invasive pest populations.

Student opportunities

We are open to applications for thesis projects! We have different thesis topics available, including projects with Fruit fly experiments, Evolutionary modelling, Population genetics, Molecular biology, and Bioinformatics. Interested? Contact Nicky.Faber@wur.nl.