A gene drive is a natural process (see meiotic drive) and technology of genetic engineering that propagates a particular suite of genes throughout a population by altering the probability that a specific allele will be transmitted to offspring (instead of the Mendelian 50% probability). Gene drives can arise through a variety of mechanisms. They have been proposed to provide an effective means of genetically modifying specific populations and entire species.
The technique can employ adding, deleting, disrupting, or modifying genes.
Proposed applications include exterminating insects that carry pathogens (notably mosquitoes that transmit malaria, dengue, and zika pathogens), controlling invasive species, or eliminating herbicide or pesticide resistance.
As with any potentially powerful technique, gene drives can be misused in a variety of ways or induce unintended consequences. For example, a gene drive intended to affect only a local population might spread across an entire species. Gene drives that eradicate populations of invasive species in their non-native habitats may have consequences for the population of the species as a whole, even in its native habitat. Any accidental return of individuals of the species to its original habitats, through natural migration, environmental disruption (storms, floods, etc.), accidental human transportation, or purposeful relocation, could unintentionally drive the species to extinction if the relocated individuals carried harmful gene drives.
Gene drives can be built from many naturally occurring selfish genetic elements that use a variety of molecular mechanisms. These naturally occurring mechanisms induce similar segregation distortion in the wild, arising when alleles evolve molecular mechanisms that give them a transmission chance greater than the normal 50%.
Most gene drives have been developed in insects, notably mosquitoes, as a way to control insect-borne pathogens. Recent developments designed gene drives directly in viruses, notably herpesviruses. These viral gene drives can propagate a modification into the population of viruses, and aim to reduce the infectivity of the virus.
Mechanism In sexually-reproducing species, most genes are present in two copies (which can be the same or different alleles), either one of which has a 50% chance of passing to a descendant. By biasing the inheritance of particular altered genes, synthetic gene drives could more effectively spread alterations through a population.
Typically, scientists insert the gene drive into an organism's DNA along with the CRISPR-Cas9 machinery. When the modified organism mates and its DNA mixes with that of its mate, the CRISPR-Cas9 tool cuts the partner's DNA at the same spot where the gene drive is located in the first organism. The cell repairs the cut DNA by copying the gene drive from the first organism into the corresponding spot in the DNA of the offspring. This means both copies of the gene (one from each parent) now contain the gene drive. This in turn means all offspring of that individual will inherit the gene drive.
Molecular mechanisms
At the molecular level, an endonuclease gene drive works by cutting a chromosome at a specific site that does not encode the drive, inducing the cell to repair the damage by copying the drive sequence onto the damaged chromosome. The cell then has two copies of the drive sequence. The method derives from genome editing techniques and relies on homologous recombination. To achieve this behavior, endonuclease gene drives consist of two nested elements:
An endonuclease that selectively cuts at the "target sequence", i.e. the rival allele. This can be one of: A homing endonuclease, which is what natural inteins use to propagate. They are, however, very difficult, if not impossible, to retarget. An RNA-guided endonuclease (e.g., Cas9 or Cas12a"Even CRISPR". The Economist. ISSN 0013-0613. Retrieved 2016-05-03. Note: Cas12a was previously known as Cpf1. The latter name is used in this 2015 article.) and its guide RNA, which can be easily altered to set the target. Cas9 is the most promising technology identified in a 2014 review. Cas9 gene drives have been successfully tested in 2015, and Cas12a in 2023. Any other programmable endonuclease system, such as modular zinc finger nucleases and TALEN. One such drive has been successfully tested in fruit flies, but it turned out to be evolutionarily unstable due to the many-repeat nature of those endonucleases. A template sequence used by the DNA repair machinery after the target sequence is cut. To achieve the self-propagating nature of gene drives, this repair template contains at least the endonuclease sequence. Because the template must be used to repair a double-strand break at the cutting site, its sides are homologous to the sequences that are adjacent to the cutting site in the host genome. By targeting the gene drive to a gene coding sequence, this gene will be inactivated; additional sequences can be introduced in the gene drive to encode new functions.
As a result, the gene drive insertion in the genome will re-occur in each organism that inherits one copy of the modification and one copy of the wild-type gene. If the gene drive is already present in the egg cell (e.g. when received from one parent), all the gametes of the individual will carry the gene drive (instead of 50% in the case of a normal gene).
Spreading in the population
Since it can never more than double in frequency with each generation, a gene drive introduced in a single individual typically requires dozens of generations to affect a substantial fraction of a population. Alternatively, releasing drive-containing organisms in sufficient numbers can affect the rest within a few generations; for instance, by introducing it in every thousandth individual, it takes only 12–15 generations to be present in all individuals. Whether a gene drive will ultimately become fixed in a population and at which speed depends on its effect on individual fitness, on the rate of allele conversion, and on the population structure. In a well mixed population and with realistic allele conversion frequencies (≈90%), population genetics predicts that gene drives get fixed for a selection coefficient smaller than 0.3; in other words, gene drives can be used to spread modifications as long as reproductive success is not reduced by more than 30%. This is in contrast with normal genes, which can only spread across large populations if they increase fitness.
Gene drive in viruses Because the strategy usually relies on the simultaneous presence of an unmodified and a gene drive allele in the same cell nucleus, it had generally been assumed that a gene drive could only be engineered in sexually reproducing organisms, excluding bacteria and viruses. However, during a viral infection, viruses can accumulate hundreds or thousands of genome copies in infected cells. Cells are frequently co-infected by multiple virions and recombination between viral genomes is a well-known and widespread source of diversity for many viruses. In particular, herpesviruses are nuclear-replicating DNA viruses with large double-stranded DNA genomes and frequently undergo homologous recombination during their replication cycle.
These properties have enabled the design of a gene drive strategy that doesn't involve sexual reproduction, instead relying on co-infection of a given cell by a naturally occurring and an engineered virus. Upon co-infection, the unmodified genome is cut and repaired by homologous recombination, producing new gene drive viruses that can progressively replace the naturally occurring population. In cell culture experiments, it was shown that a viral gene drive can spread into the viral population and strongly reduce the infectivity of the virus, which opens novel therapeutic strategies against herpesviruses.
Technical limitations Because gene drives propagate by replacing other alleles that contain a cutting site and the corresponding homologies, their application has been mostly limited to sexually reproducing species (because they are diploid or polyploid and alleles are mixed at each generation). As a side effect, inbreeding could in principle be an escape mechanism, but the extent to which this can happen in practice is difficult to evaluate.
Due to the number of generations required for a gene drive to affect an entire population, the time to universality varies according to the reproductive cycle of each species: it may require under a year for some invertebrates, but centuries for organisms with years-long intervals between birth and sexual maturity, such as humans. Hence this technology is of most use in fast-reproducing species.
Effectiveness in real practice varies between techniques, especially by choice of germline promoter. Lin and Potter 2016 (a) discloses the promoter technology homology assisted CRISPR knockin (HACK) and Lin and Potter 2016 (b) demonstrates actual use, achieving a high proportion of altered progeny from each altered Drosophila mother.
Issues Issues highlighted by researchers include:
Mutations: A mutation could happen mid-drive, which has the potential to allow unwanted traits to "ride along". Escape: Cross-breeding or gene flow potentially allow a drive to move beyond its target population. Ecological impacts: Even when new traits' direct impact on a target is understood, the drive may have side effects on the surroundings.
The Broad Institute of MIT and Harvard added gene drives to a list of uses of gene-editing technology it doesn't think companies should pursue.
Bioethics concerns Gene drives affect all future generations and represent the possibility of a larger change in a living species than has been possible before. "I don't care if it's a weed or a blight, people still are going to say this is way too massive a genetic engineering project," [bioethicist] Caplan says. "Secondly, it's altering things that are inherited, and that's always been a bright line for genetic engineering."
In December 2015, scientists of major world academies called for a moratorium on inheritable human genome edits that would affect the germline, including those related to CRISPR-Cas9 technologies, but supported continued basic research and gene editing that would not affect future generations. In February 2016, British scientists were given permission by regulators to genetically modify human embryos by using CRISPR-Cas9 and related techniques on condition that the embryos were destroyed in seven days. In June 2016, the US National Academies of Sciences, Engineering, and Medicine released a report on their "Recommendations for Responsible Conduct" of gene drives.
A 2018 mathematical modelling studies suggest that despite preexisting and evolving gene drive resistance (caused by mutations at the cutting site), even an inefficient CRISPR "alteration-type" gene drive can achieve fixation in small populations. With a small but non-zero amount of gene flow among many local populations, the gene drive can escape and convert outside populations as well.