Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2020 Mar 12;18(1):27.
doi: 10.1186/s12915-020-0761-2.

Performance Analysis of Novel Toxin-Antidote CRISPR Gene Drive Systems

Affiliations
Free PMC article

Performance Analysis of Novel Toxin-Antidote CRISPR Gene Drive Systems

Jackson Champer et al. BMC Biol. .
Free PMC article

Abstract

Background: CRISPR gene drive systems allow the rapid spread of a genetic construct throughout a population. Such systems promise novel strategies for the management of vector-borne diseases and invasive species by suppressing a target population or modifying it with a desired trait. However, current homing-type drives have two potential shortcomings. First, they can be thwarted by the rapid evolution of resistance. Second, they lack any mechanism for confinement to a specific target population. In this study, we conduct a comprehensive performance assessment of several new types of CRISPR-based gene drive systems employing toxin-antidote (TA) principles, which should be less prone to resistance and allow for the confinement of drives to a target population due to invasion frequency thresholds.

Results: The underlying principle of the proposed CRISPR toxin-antidote gene drives is to disrupt an essential target gene while also providing rescue by a recoded version of the target as part of the drive allele. Thus, drive alleles tend to remain viable, while wild-type targets are disrupted and often rendered nonviable, thereby increasing the relative frequency of the drive allele. Using individual-based simulations, we show that Toxin-Antidote Recessive Embryo (TARE) drives targeting an haplosufficient but essential gene (lethal when both copies are disrupted) can enable the design of robust, regionally confined population modification strategies with high flexibility in choosing promoters and targets. Toxin-Antidote Dominant Embryo (TADE) drives require a haplolethal target gene and a germline-restricted promoter, but they could permit faster regional population modification and even regionally confined population suppression. Toxin-Antidote Dominant Sperm (TADS) drives can be used for population modification or suppression. These drives are expected to spread rapidly and could employ a variety of promoters, but unlike TARE and TADE, they would not be regionally confined and also require highly specific target genes.

Conclusions: Overall, our results suggest that CRISPR-based TA gene drives provide promising candidates for flexible ecological engineering strategies in a variety of organisms.

Keywords: Biotechnology; CRISPR; Confined; Gene drive; Modeling; Population modification; Population suppression; Toxin-antidote.

Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Overview of TA systems and performance characteristics. a Illustration of viable and nonviable genotypes for the different types of TA systems. b TARE, TADE, TADDE, and Medea drives have fitness-dependent introduction thresholds, above which the drive will increase in frequency and below which it will decrease. Frequencies represent the introduction of drive heterozygotes (with “ideal” drives in the deterministic model). The black dotted line shows the final drive allele equilibrium frequency for TARE, TADDE, and Medea, though all individuals should carry at least one copy of the drive at these equilibria. c Migration thresholds for the different TA systems, showing the per generation influx of new migrants (homozygotes for TARE, TADE, and TADDE, heterozygotes for TADE suppression) as a fraction of the population that is required for the drive to eventually spread to all individuals in the population (below this level, the drive reaches a low equilibrium frequency). Note that these thresholds likely overestimate the invasion potential of a TADE suppression system, since suppression and subsequent reduction in migration will occur in distant populations that send migrants as the drive increases in frequency. d The genetic load imposed by idealized TA drives as a function of the drive homozygote fitness in the deterministic model. Eradication will only occur if the genetic load can overcome the fitness advantage of individuals at low population density. Note that “TARE and TADDE suppression drive” refers to a distant-site TARE or TADDE drive located in a female fertility gene (as in a TADE suppression drive). Such a drive reaches a moderate equilibrium frequency and is thus unable to impose a large genetic load on the population like a TADE suppression drive
Fig. 2
Fig. 2
TARE drive. a In the TARE drive, germline activity disrupts the target gene, followed by embryo activity in the progeny of drive-carrying females. The target gene is assumed to be essential and haplosufficient, so any individuals inheriting two disrupted (recessive lethal) target genes are nonviable. By contrast, all individuals with at least one wild-type or drive allele are assumed to be viable. b The speed at which a TARE drive is expected to reach 99% of individuals in the population with varying introduction frequency and drive fitness. The dashed line indicates the introduction frequency threshold in the deterministic model. c Same as b, but with varying germline and embryo cleavage rates. Gray means that the drive failed to reach 99% because it spread too slowly or was not able to spread at all
Fig. 3
Fig. 3
TADE drive. a In the TADE drive, germline activity disrupts the target gene, and the nuclease promoter is selected to minimize embryo activity. The target gene is assumed to be haplolethal, so any individuals inheriting one disrupted target allele will be nonviable, even if the other allele is drive or wild-type. b The speed at which a TADE drive is expected to reach 99% of individuals in the population with varying introduction frequency and drive fitness. The dashed line indicates the introduction frequency threshold in the deterministic model. c Same as b, but with varying germline and embryo cleavage rate
Fig. 4
Fig. 4
TADE suppression drive. a The target gene of a TADE suppression drive is at a different site from the drive allele (modeled as an unlinked site), which is located in a female (or male) fertility gene. The drive disrupts the fertility gene, so female drive homozygotes are sterile (“drive homozygote fitness” does not apply). Germline activity disrupts the target gene, and the nuclease promoter is selected to minimize embryo activity. The target gene is haplolethal, so any individuals inheriting fewer than two wild-type target alleles and/or drive alleles are nonviable. b The genetic load imposed by a TADE suppression drive in our deterministic model. If the germline cleavage rate is 100%, eradication will occur. Otherwise, eradication will only occur if the genetic load can overcome the fitness advantage of individuals at low population density. Note that this drive loses the ability to increase in frequency in any population when the germline cut rate is very low. c The speed at which the TADE suppression drive reaches 99% of individuals in the population with varying introduction frequency and drive fitness. Full suppression or an equilibrium state will be attained within a few generations of this point. The dashed line indicates the introduction frequency threshold in the deterministic model. d Same as c, but with varying germline and embryo cleavage rate
Fig. 5
Fig. 5
TADDE drive. a In the TADDE drive, germline activity disrupts the target gene, and embryo activity is optional (and preferred unless germline cleavage is 100%). The target gene is haplolethal, so any individuals inheriting at least one disrupted target allele are nonviable unless they also inherit a drive allele, which encodes two copies of the gene or provides sufficient expression of the target gene such that only one copy is needed for rescue. b The speed at which the TADDE drive is expected to reach 99% of individuals in the population with varying introduction frequency and drive fitness. The dashed line indicates the introduction frequency threshold in the deterministic model. c Same as b, but with varying germline and embryo cleavage rate
Fig. 6
Fig. 6
TADS drive. a In the TADS drive, germline activity disrupts the target gene, followed by embryo activity in the progeny of drive-carrying females. The target gene is expressed in male gametocytes after meiosis I, and such expression is necessary for development of a viable sperm. Thus, sperm with a disrupted allele are nonviable, and only sperm with a wild-type or drive allele are viable. b The speed at which the TADS drive is expected to reach 99% of individuals in the population with varying introduction frequency and drive fitness. c Same as b, but with varying germline and embryo cleavage rate
Fig. 7
Fig. 7
TADS suppression drive. a The TADS suppression drive is distant-site, located in a male fertility gene and modeled here with a target gene that is unlinked from the drive allele. Male drive homozygotes are thus sterile (“drive homozygote fitness” does not apply). Germline activity disrupts the target gene, followed by embryo activity in the progeny of drive-carrying females. The target gene is expressed in male gametocytes after meiosis I, and such expression is necessary for the development of a viable sperm. Thus, sperm with a disrupted target allele are nonviable unless they also have a drive allele. b The speed at which the TADS suppression drive is expected to reach 99% of individuals in the population with varying introduction frequency and drive fitness. Full suppression would occur within a few generations of this point. c Same as b, but with varying germline and embryo cleavage rate
Fig. 8
Fig. 8
TADS Y-linked suppression drive. a The TADS Y-linked suppression drive is distant-site. It is located on the Y chromosome and has a target gene that is not linked to the drive allele (modeled here to be on an autosomal chromosome). Germline activity disrupts the target gene, followed by embryo activity in the progeny of drive-carrying females. The target gene has expression in male gametocytes after meiosis I, and such expression is necessary for development of a viable sperm. Thus, sperm with a disrupted target allele are nonviable unless they also have a drive allele. b The ability of the TADS Y-linked suppression drive to suppress a population in our deterministic model. If the germline cleavage rate is 100%, suppression will occur. Otherwise, suppression will occur only if the genetic load can overcome the fitness advantage of individuals at low population density. c The speed at which the TADS suppression drive is expected to reach 99% of individuals in the population with varying introduction frequency and drive fitness. Full suppression or an equilibrium state will be attained within a few generations of this point. d Same as c, but with varying germline cleavage rate (the Y-linked drive can only be carried by males, so there would likely not be any embryo cleavage—however, if there was paternal activity due to unusually high nuclease/gRNA expression or stability, this would be expected to further increase drive efficiency)
Fig. 9
Fig. 9
Resistance to TA systems. Analysis was conducted for drive systems with 100% cleavage rates (germline only for TADE) and 95% drive homozygote fitness. Each cleavage event was assumed to result in a functional r1 allele instead of a disrupted target allele with 10% probability. The number of gRNAs was varied, and a resistance allele was considered to be a “complete” r1 allele only if all gRNA cleavage sites possessed r1 sequences. The vertical axis shows the frequency of complete r1 alleles after 100 generations

Similar articles

See all similar articles

References

    1. Esvelt KM, Smidler AL, Catteruccia F, Church GM. Concerning RNA-guided gene drives for the alteration of wild populations. Elife. 2014;:e03401. doi:10.7554/eLife.03401. - PMC - PubMed
    1. Champer J, Buchman A, Akbari OS. Cheating evolution: engineering gene drives to manipulate the fate of wild populations. Nat Rev Genet. 2016;17:146–159. doi: 10.1038/nrg.2015.34. - DOI - PubMed
    1. Burt A. Heritable strategies for controlling insect vectors of disease. Philos Trans R Soc L B Biol Sci. 2014;369:20130432. doi: 10.1098/rstb.2013.0432. - DOI - PMC - PubMed
    1. Unckless RL, Messer PW, Connallon T, Clark AG. Modeling the manipulation of natural populations by the mutagenic chain reaction. Genetics. 2015;201:425–431. doi: 10.1534/genetics.115.177592. - DOI - PMC - PubMed
    1. Alphey L. Genetic control of mosquitoes. Annu Rev Entomol. 2014;59:205–224. doi: 10.1146/annurev-ento-011613-162002. - DOI - PubMed

Publication types

LinkOut - more resources

Feedback