A toxin-antidote CRISPR gene drive system for regional population modification

Engineered gene drives based on a homing mechanism could rapidly spread genetic alterations through a population. However, such drives face a major obstacle in the form of resistance against the drive. In addition, they are expected to be highly invasive. Here, we introduce the Toxin-Antidote Recessive Embryo (TARE) drive. It functions by disrupting a target gene, forming recessive lethal alleles, while rescuing drive-carrying individuals with a recoded version of the target. Modeling shows that such drives will have threshold-dependent invasion dynamics, spreading only when introduced above a fitness-dependent frequency. We demonstrate a TARE drive in Drosophila with 88-95% transmission by female heterozygotes. This drive was able to spread through a large cage population in just six generations following introduction at 24% frequency without any apparent evolution of resistance. Our results suggest that TARE drives constitute promising candidates for the development of effective, flexible, and regionally confinable drives for population modification. CRISPR homing gene drives are highly invasive and can fail due to the rapid evolution of resistance. Here the authors present TARE drive, inspired by naturally occurring selfish genetic elements, which is less vulnerable to resistance and can potentially be confined to a target population.

[1]  Ethan Bier,et al.  The mutagenic chain reaction: A method for converting heterozygous to homozygous mutations , 2015, Science.

[2]  Rachael M. Giersch,et al.  Tuning CRISPR-Cas9 Gene Drives in Saccharomyces cerevisiae , 2018, G3: Genes, Genomes, Genetics.

[3]  James J. Collins,et al.  A CRISPR Cas9-based gene drive platform for genetic interaction analysis in Candida albicans , 2017, Nature Microbiology.

[4]  John M. Marshall,et al.  Medusa: A Novel Gene Drive System for Confined Suppression of Insect Populations , 2014, PloS one.

[5]  R. Beeman,et al.  Properties and natural occurrence of maternal-effect selfish genes (‘Medea’ factors) in the Red Flour Beetle, Tribolium castaneum , 1999, Heredity.

[6]  Héctor M. Sánchez C.,et al.  Consequences of resistance evolution in a Cas9-based sex conversion-suppression gene drive for insect pest management , 2018, Proceedings of the National Academy of Sciences.

[7]  N. Gemmell,et al.  Conservation demands safe gene drive , 2017, PLoS biology.

[8]  John M. Marshall,et al.  GENERAL PRINCIPLES OF SINGLE-CONSTRUCT CHROMOSOMAL GENE DRIVE , 2012, Evolution; international journal of organic evolution.

[9]  F. Reed,et al.  First Steps towards Underdominant Genetic Transformation of Insect Populations , 2014, PloS one.

[10]  Georg Oberhofer,et al.  Behavior of homing endonuclease gene drives targeting genes required for viability or female fertility with multiplexed guide RNAs , 2018, Proceedings of the National Academy of Sciences.

[11]  Lorian Schaeffer,et al.  A Synthetic Maternal-Effect Selfish Genetic Element Drives Population Replacement in Drosophila , 2007, Science.

[12]  A. Burt,et al.  Gene Drive: Evolved and Synthetic , 2018, ACS chemical biology.

[13]  Ethan Bier,et al.  Highly efficient Cas9-mediated gene drive for population modification of the malaria vector mosquito Anopheles stephensi , 2015, Proceedings of the National Academy of Sciences.

[14]  Andrew G. Clark,et al.  Reducing resistance allele formation in CRISPR gene drive , 2018, Proceedings of the National Academy of Sciences.

[15]  Philipp W. Messer,et al.  CRISPR Gene Drive Efficiency and Resistance Rate Is Highly Heritable with No Common Genetic Loci of Large Effect , 2019, Genetics.

[16]  Philipp W. Messer,et al.  Novel CRISPR/Cas9 gene drive constructs reveal insights into mechanisms of resistance allele formation and drive efficiency in genetically diverse populations , 2017, PLoS genetics.

[17]  Austin Burt,et al.  Heritable strategies for controlling insect vectors of disease , 2014, Philosophical Transactions of the Royal Society B: Biological Sciences.

[18]  John M. Marshall,et al.  The effect of gene drive on containment of transgenic mosquitoes. , 2009, Journal of theoretical biology.

[19]  Philipp W. Messer,et al.  Molecular safeguarding of CRISPR gene drive experiments , 2018, bioRxiv.

[20]  Jackson Champer,et al.  Cheating evolution: engineering gene drives to manipulate the fate of wild populations , 2016, Nature Reviews Genetics.

[21]  A. Burt,et al.  A CRISPR–Cas9 gene drive targeting doublesex causes complete population suppression in caged Anopheles gambiae mosquitoes , 2018, Nature Biotechnology.

[22]  Bruce A. Hay,et al.  Cleave and Rescue, a novel selfish genetic element and general strategy for gene drive , 2019, Proceedings of the National Academy of Sciences.

[23]  Fred Gould,et al.  MEDEA SELFISH GENETIC ELEMENTS AS TOOLS FOR ALTERING TRAITS OF WILD POPULATIONS: A THEORETICAL ANALYSIS , 2011, Evolution; international journal of organic evolution.

[24]  Andrea Crisanti,et al.  The creation and selection of mutations resistant to a gene drive over multiple generations in the malaria mosquito , 2017, bioRxiv.

[25]  Andrew G. Clark,et al.  Performance analysis of novel toxin-antidote CRISPR gene drive systems , 2019, BMC Biology.

[26]  Austin Burt,et al.  Requirements for effective malaria control with homing endonuclease genes , 2011, Proceedings of the National Academy of Sciences.

[27]  Population dynamics of underdominance gene drive systems in continuous space. , 2020, ACS synthetic biology.

[28]  John M. Marshall,et al.  The toxin and antidote puzzle , 2011, Bioengineered bugs.

[29]  Andrew G. Clark,et al.  Computational and experimental performance of CRISPR homing gene drive strategies with multiplexed gRNAs , 2019, Science Advances.

[30]  A. Burt,et al.  Modelling the potential of genetic control of malaria mosquitoes at national scale , 2019, BMC Biology.

[31]  Rachael M. Giersch,et al.  Gene drive inhibition by the anti-CRISPR proteins AcrIIA2 and AcrIIA4 in Saccharomyces cerevisiae , 2018, Microbiology.

[32]  Ben Adlam,et al.  Current CRISPR gene drive systems are likely to be highly invasive in wild populations , 2017, bioRxiv.

[33]  Arne Traulsen,et al.  Using underdominance to bi-stably transform local populations. , 2010, Journal of theoretical biology.

[34]  Melissa M. Harrison,et al.  Genome Engineering of Drosophila with the CRISPR RNA-Guided Cas9 Nuclease , 2013, Genetics.

[35]  Martin A. Nowak,et al.  Evolutionary dynamics of CRISPR gene drives , 2016, Science Advances.

[36]  Andrea Crisanti,et al.  A CRISPR-Cas9 Gene Drive System Targeting Female Reproduction in the Malaria Mosquito vector Anopheles gambiae , 2015, Nature Biotechnology.

[37]  John M. Marshall,et al.  Confinement of gene drive systems to local populations: a comparative analysis. , 2012, Journal of theoretical biology.

[38]  Yunmei Ma,et al.  Temporally and biochemically distinct activities of Exo1 during meiosis: double-strand break resection and resolution of double Holliday junctions. , 2010, Molecular cell.

[39]  George M Church,et al.  Concerning RNA-guided gene drives for the alteration of wild populations , 2014, bioRxiv.

[40]  L. Alphey Genetic control of mosquitoes. , 2014, Annual review of entomology.

[41]  Gunnar H. D. Poplawski,et al.  Super-Mendelian inheritance mediated by CRISPR/Cas9 in the female mouse germline , 2018, Nature.

[42]  John M. Marshall,et al.  Semele: A Killer-Male, Rescue-Female System for Suppression and Replacement of Insect Disease Vector Populations , 2011, Genetics.

[43]  Fred Gould,et al.  A Killer–Rescue system for self-limiting gene drive of anti-pathogen constructs , 2008, Proceedings of the Royal Society B: Biological Sciences.

[44]  Arne Traulsen,et al.  Stability Properties of Underdominance in Finite Subdivided Populations , 2011, PLoS Comput. Biol..

[45]  Simon L. Bullock,et al.  Augmenting CRISPR applications in Drosophila with tRNA-flanked sgRNAs , 2016, Nature Methods.

[46]  Philipp W. Messer,et al.  Modeling the Manipulation of Natural Populations by the Mutagenic Chain Reaction , 2015, Genetics.

[47]  Georg Oberhofer,et al.  Gene drive and resilience through renewal with next generation Cleave and Rescue selfish genetic elements , 2019, Proceedings of the National Academy of Sciences.

[48]  M J Wade,et al.  The population dynamics of maternal-effect selfish genes. , 1994, Genetics.

[49]  Matthew P. Edgington,et al.  Population dynamics of engineered underdominance and killer-rescue gene drives in the control of disease vectors , 2018, PLoS Comput. Biol..

[50]  Simon L. Bullock,et al.  Optimized CRISPR/Cas tools for efficient germline and somatic genome engineering in Drosophila , 2014, Proceedings of the National Academy of Sciences.

[51]  Fred Gould,et al.  Tethered homing gene drives: A new design for spatially restricted population replacement and suppression , 2018, bioRxiv.

[52]  C. Rubinstein,et al.  Highly Specific and Efficient CRISPR/Cas9-Catalyzed Homology-Directed Repair in Drosophila , 2014, Genetics.

[53]  Andrea Crisanti,et al.  Improved CRISPR-based suppression gene drives mitigate resistance and impose a large reproductive load on laboratory-contained mosquito populations , 2018, bioRxiv.

[54]  John M. Marshall,et al.  Inverse Medea as a Novel Gene Drive System for Local Population Replacement: A Theoretical Analysis , 2011, The Journal of heredity.

[55]  James E. DiCarlo,et al.  Safeguarding CRISPR-Cas9 gene drives in yeast , 2015, Nature Biotechnology.

[56]  Fred Gould,et al.  Invasion and migration of spatially self‐limiting gene drives: A comparative analysis , 2018, Evolutionary applications.

[57]  Lorian Schaeffer,et al.  A synthetic maternal-effect selfish genetic element drives population replacement in Drosophila. , 2007, Science.