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  • Review Article
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Gene drives gaining speed

Nature Reviews Genetics volumeΒ 23,Β pages 5–22 (2022) Cite this article

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Abstract

Gene drives are selfish genetic elements that are transmitted to progeny at super-Mendelian (>50%) frequencies. Recently developed CRISPR–Cas9-based gene-drive systems are highly efficient in laboratory settings, offering the potential to reduce the prevalence of vector-borne diseases, crop pests and non-native invasive species. However, concerns have been raised regarding the potential unintended impacts of gene-drive systems. This Review summarizes the phenomenal progress in this field, focusing on optimal design features for full-drive elements (drives with linked Cas9 and guide RNA components) that either suppress target mosquito populations or modify them to prevent pathogen transmission, allelic drives for updating genetic elements, mitigating strategies including trans-complementing split-drives and genetic neutralizing elements, and the adaptation of drive technology to other organisms. These scientific advances, combined with ethical and social considerations, will facilitate the transparent and responsible advancement of these technologies towards field implementation.

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Fig. 1: Design and spread of CRISPR-based gene drives.
Fig. 2: Suppression drives and mathematical modelling.
Fig. 3: Modification drives and mathematical modelling.
Fig. 4: Alternative and neutralizing drives.
Fig. 5: The road forwards.

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Acknowledgements

These studies were supported by NIH grant R01 GM117321, a Paul G. Allen Frontiers Group Distinguished Investigator Award to E.B., the Bill and Melinda Gates Foundation and a gift from the Tata Trusts in India to TIGS-UCSD. The author thanks his UCI-Malaria Initiative colleagues: A. A. James, G. Dimopoulos, G. Lanzaro, A. Kormos, and J. Marshall for thoughtful discussions and comments on the manuscript as well as A. A. James and A. Crisanti for granting permission to cite some of their unpublished results.

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    Ethan Bier

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E.B. has equity interest in two companies: Synbal Inc. and Agragene, Inc. These companies may potentially benefit from the research results. E.B. also serves on Synbal Inc.’s Board of Directors and Scientific Advisory Board and on Agragene Inc.’s Scientific Advisory Board. The terms of these arrangements have been reviewed and approved by the University of California, San Diego, in accordance with its conflict of interest policies.

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TIGS: Tata Institutes for Genetics and Society, UCSD: https://tigs.ucsd.edu/

UCIMI: University of California Irvine Malaria Initiative: https://ucimi.org/

WHO Guidelines for malaria: https://app.magicapp.org/#/guideline/5438

WHO Malaria: https://www.who.int/news-room/fact-sheets/detail/malaria

WHO World Malaria Report 2019: https://www.who.int/publications/i/item/9789241565721

Supplementary information

Glossary

Gene drives

An allele of a diploid gene experiences gene drive if it is inherited more than 50% of the time (that is, more than by random chance).

High-threshold drives

Drive systems wherein release of many individuals is required for super-Mendelian spread of the drive.

Low-threshold drives

Drive systems wherein the release of only a few individuals is required for super-Mendelian spread of the drive.

Essential gene

A gene required for the viability or reproduction of an organism.

Homology-directed repair

(HDR). A DNA repair pathway initiated following induction of double-strand DNA breaks in which the break is repaired by copying sequences (or a template) from an identical sister chromosome (typically following DNA replication in somatic cells) or from the homologous chromosome (typically during meiosis, although sometimes also in somatic cells).

Anopheline mosquitoes

A genus of mosquitoes that carry malarial parasites.

CRISPR

A bacterial immunity system from which the synthetic CRISPR–Cas9 genome editing system was derived by Jenifer Doudna and colleagues.

Guide RNA

(gRNA). A synthetic linkage of two RNA components of bacterial CRISPR systems: transactivating CRISPR RNA and CRISPR RNA. gRNAs are sometimes also denoted sgRNA (synthetic-guide RNA or single-guide RNA).

Anti-malarial effectors

Transgenes encoding proteins that, when expressed, exert a desired anti-malarial effect, such as for anti-malarial peptides expressed following a blood meal in mosquitoes.

Trans-complementing drive

A split CRISPR-based gene-drive system comprising two components: a Cas9-expressing element and a guide RNA (gRNA)-bearing element that are inserted at different sites in the genome. The gRNA element carries two gRNAs, one to copy itself and the other cutting at the insertion site of the Cas9 element. Alone, each element is inherited in a standard Mendelian fashion. When combined, however, the gRNAs complex with Cas9 provided in trans to drive copying of both elements, thereby creating a full-drive system that efficiently transmits both elements toΒ progeny.

Neutralizing drives

Genetic elements designed to eliminate or halt the spread of a gene drive. Examples include active guide RNA (gRNA)-only elements such as e-CHACRs (erasing constructs hitchhiking on the autocatalytic chain reaction), ERACRs (elements reversing the autocatalytic chain reaction) or Cas9-triggered chain ablation (CATCHA) elements, anti-Cas9 proteins, as well as passive recoded fitness-neutral gRNA target sites (for replacing suppression drives).

Active genetics

Copying of a genetic element from one chromosome to its homologue in response to a double-strand DNA break being generated in the homologue at the same genomic site where the active genetic element is inserted. Copying, which results from directional gene conversion, is typically mediated in the germline by the synthesis-dependent strand annealing (or D-loop) branch of the homology-directed repair pathway.

Suppression drives

Gene drives that reduce the size of the target population. Typically, suppression drives insert into genes required for the viability or fertility of one or both sexes.

Malaria

An infectious blood disease caused by Plasmodial parasites (for example, Plasmodium falciparum and Plasmodium vivax) that is primarily transmitted (vectored) by mosquitoes in the Anopheline genus.

Aedes mosquitoes

A genus of mosquitoes carrying arboviruses that transmit dengue fever, yellow fever, chikungunya or Zika.

Modification drives

Also referred to as replacement drives. Drive systems that modify a target population but do not reduce its numbers.

Non-homologous end-joining

(NHEJ). A DNA repair pathway initiated following the induction of double-strand DNA breaks in which the two ends of DNA are ligated back to each other in a template-independent fashion. NHEJ can introduce small insertions or deletions, which can cause mutations and frameshift-based loss-of-function alleles of a gene.

Basic reproductive number

(R0). The expected number of disease cases generated by one person infected with a pathogen if all individuals are susceptible to infection (that is, at the beginning of disease spread). For vector-borne diseases, it depends on several factors involving the vector hosts as well as infected persons (BoxΒ 1).

Introduction

The full introduction of a specific allele from one genetic background into another results in all progeny carrying the allele in question. The term introgression, typically of a trait that is potentially associated with additional surrounding local genetic variation from one strain into another background, can also be used in such contexts. Example 1: a gene-drive element carried in one strain that spreads to 100% introduction throughout a naive target population. Example 2: an insecticide-resistant allele and a neighbouring 1 megabase region were introgressed into a sensitive strain of mosquitoes from a resistant strain.

Recoded drives

Gene drives that carry a recoded version of a target gene into which it inserts such that the recoded sequences at the 5Β΄ end of the drive element are fused seamlessly to endogenous coding sequences, restoring wild-type protein activity and expression of the endogenous gene.

CHACRs

(Constructs hitchhiking on the autocatalytic chain reaction). Active genetic elements carrying a guide RNA to copy themselves and potential cargo but no Cas9 source.

Allelic drives

Genetic systems biasing the inheritance of a particular allelic variant, typically altering only one or a few base pairs. CRISPR-based allelic-drive systems can be of two types, copy-cutting or copy-grafting.

e-CHACR

(erasing construct hitchhiking on the autocatalytic chain reaction). A drive-neutralizing active genetic element that encodes two or more guide RNAs (gRNAs) but no source of Cas9. One of the gRNAs cuts at the genomic site of e-CHACR insertion, enabling self-copying in the presence of a trans-acting source of Cas9 provided by the gene drive. The additional gRNAs target cleavage and inactivation of the Cas9 transgene component of a gene-drive element. e-CHACRs can be inserted into the genome at any desired location.

Copy-cutting

A form of allelic drive in which the driving guide RNA directly cuts the non-preferred allelic variant, leaving the preferred allele intact.

Copy-grafting

A form of allelic drive in which the preferred allele is adjacent to a sequence immune to cleavage by a guide RNA (gRNA) that can cut wild-type or non-preferred alleles. When the gRNA cuts either the wild-type or non-preferred allelic variants, the double-strand break is repaired by homology-directed repair (HDR) using the cleavage-resistant allele as a template, copying the favoured allelic variant in the process. The cleavage-resistant gRNA site and preferred allele are typically <25 bp apart to be copied reliably together as a by-product of the short-range end-resection step of HDR.

ERACRs

(Element reversing the autocatalytic chain reaction). Drive-neutralizing active genetic elements that encode two guide RNAs cutting on either side of the gene-drive element. ERACRs are inserted at the same genomic site as the drive elements they are designed to delete and replace. ERACRs can carry additional cargo such as recoded copies of a gene targeted for disruption by the gene drive. However, ERACRs do not carry a Cas9 source.

Allo-alleles

Alleles in a polyploid species (allopolyploid or autoploid) whose chromosomes either derive from whole-genome duplications within a species (autoploidy) or result from the fusion of two different genomes (alloploidy) followed by the potential partial loss of genetic information. Many crop species such as grains (wheat, rye), corn, peanuts and sugarcane are polyploid as are a few animal species (for example, Xenopus laevis (African clawed frogs)).

Culex mosquitoes

A genus of mosquitoes serving as vectors for diseases, including West Nile fever, St Louis encephalitis, Japanese encephalitis, and viral diseases in birds and horses.

World Health Organization phases of gene-drive development

The phases are as follows. Phase 1 is laboratory development and testing. Phase 2 is confined outdoor tests (either in large cages or isolated environments such as islands); the goal of these experiments is to achieve defined entomological endpoints such as a certain percentage of population reduction (suppression) or drive introgression (modification). Phase 3 is limited testing in disease-endemic regions to demonstrate epidemiological efficacy. Phase 4 is full implementation.

Risk assessment

A formal analysis of all factors that need to be considered, evaluated and balanced before implementing an intervention such as the release of organisms carrying a gene-drive element. Risks should include predicted or potential consequences associated with performing the intervention as well as those accompanying a decision not to implement the technology.

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Bier, E. Gene drives gaining speed. Nat Rev Genet 23, 5–22 (2022). https://doi.org/10.1038/s41576-021-00386-0

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