Advanced Gene Editing Technologies, GMO 2.0

GMO 2.0: Synthetic Biology, Gene Editing and Gene Drives

Modern Genetic Technology: what it is and how it is regulated. (2023) Well-NZ report on economics of staying GE Free

Gene Editing Report (2023) Navdanya report critiques gene editing techniques and their effects on the natural environment

Integration of omics analyses into GMO risk assessment in Europe: a case study from soybean field trials. (2023) Environ Sci Eur 35, 14. Benevenuto et al. findings into unintended effects of GE using untargeted "omics" technologies. (https://doi.org/10.1186/s12302-023-00715-6)

Comprehensive analysis and accurate quantification of unintended large gene modifications induced by CRISPR-Cas9 gene editing (2022) Sci Adv. 8(42) Park SH, et al findings for CRISPR-Cas9 genome editing can induce large gene modifications, such as deletions, insertions, and complex local rearrangements in different primary cells and cell lines.

New genomic techniques (NGTs): agriculture, food production and crucial regulatory issues (2022) Christoph Then from Testbiotech discusses the different gene edited types.

Target-enriched nanopore sequencing and de novo assembly reveals co-occurrences of complex on-target genomic rearrangements induced by CRISPR-Cas9 in human cells (2022) Geng K et al describe their finding of extensive genomic disruptions by Cas9, involving the allelic co-occurrence of a genomic duplication and inversion of the target region, as well as integrations of exogenous DNA and clustered interchromosomal DNA fragment rearrangements. Genome Res. 32: 1876-1891(abstract)

TP53-dependent toxicity of CRISPR/Cas9 cuts is differential across genomic loci and can confound genetic screening (2022) Nature Communications, Dr Alvarez et al findings on the toxicity of double stranded breaks and loss of cell fitness

CRISPR-Cas9 editing of the arginine–vasopressin V1a receptor produces paradoxical changes in social behaviour in Syrian hamsters (2022) PNAS, Neuroscience, Taylor et al research found that hamsters aggressive behaviour toward same sex animals was caused by gene editing.

Unintended effects caused by techniques of new genetic engineering create a new quality of hazards and risks (2022) Testbiotech and Canadian Biotechnology Action Network (cban) outline the evidence that gene edited, intended and unintended genetic changes, can go far beyond previous GE methods. Many potential intended and unintended effects are specific to the new GE and may result in a new quality of risks that demand independent and mandatory risk assessment.

Fast-track to failure: Will new GMOs reduce pesticide use?... NO! (2022) Friends of the Earth report based on the evidence find new GM crops will not reduce pesticide use. Some are designed to increase it.

Synthetic Biology Technical Report Series 100 (2022) The Convention on Biodiversity (CBD) detailed report discusses the ethical, social and environmental benefits and concerns of Synthetic Biology genetic engineering

Whole chromosome loss and genomic instability in mouse embryos after CRISPR-Cas9 genome editing (2021) Nature Communications 12:5855. Papathanasiou S., Markoulaki S., Blaine L. J., Leibowitz, M. L. et al. demonstrated that Cas9-mediated germline genome editing can lead to unwanted on-target side effects, including major chromosome structural alterations that can be propagated over several divisions of embryonic development.

An Editing-Site-Specific PCR Method for Detection and Quantification of CAO1-Edited Rice (2021) Foods, Zhang et al developed an editing-site-specific PCR method presents a promising detection and quantification technique for genome-edited plants with known edited sequence

The Generic Risks and the Potential of SDN-1 Applications in Crop Plants. (2021) Plants,10, 2259. Kawall research into complex genomic alterations induced by SDN-1 applications

Chromothripsis as an on-target consequence of CRISPR–Cas9 genome editing. (2021) Nat Genet 53, Leibowitz et al research finding: gene editing causes fragmentation of the chromosome leading to tens to thousands of chromosomal rearrangements causing nucleus, micronucleus, and chromosome defects which initiate a mutational process, called Chromothripsis.

Differentiated impacts of human interventions on nature: Scaling the conversation on regulation of gene technologies (2021) Elementa, Heinemann, J.A., Paull D.J., Walker S., and Kurenbach B,. Heinemann et al provide a rationale for, and bridge to, a consistent and comprehensive approach to gene technology regulation.

Genetically Modified Microbes:Technological and Legislative Challenges and National Security Implications (2021) IRT and Protect Nature Now. Report highlights the dangers of GE microbes and their impact on the environment, psychological and social effects.

Genome-edited Camelina sativa with a unique fatty acid content and its potential impact on ecosystems (2021) Environ Sci Eur 33, 38. Dr Katharina Kawall research found that intended genome edits unintentionally alter the composition of a plant and/or interfere with its metabolism.

Accurate Detection and Evaluation of the Gene-Editing Frequency in Plants Using Droplet Digital PCR (2020) Front. Plant Sci. Peng C., et al research on the accuracy and precision of duplexed dPCR assay tool for the detection and evaluation of gene-editing frequencies in plants in gene-editing technology.

Anticipating and Identifying Collateral Damage in Genome Editing (2020),Trends in Genetics, Burgio and Teboul critical appraisal of benefits and risks associated with genome technologies.

Gene-Silencing Pesticides: Risks and Concerns (2020) Friends of the Earth (FOE). Dr. Sirinathsinghji, Klein, Dana Perls, M.C.P., have written a comprehensive and clear report on RNAi technologies and the risks they pose.

RNA-based pesticides aim to get around resistance problems (2020) PNAS, Shaffer L article discusses the new ways RNAi pesticides will work after weeds and pests have become to resistant to the herbicides and pesticides used on GM crops

Investigation of CRISPR/Cas9-induced SD1 rice mutants highlights the importance of molecular characterization in plant molecular breeding (2020) Biswas S., Tian J., Li R., Chen X., Luo Z. et al article finding imprecision CRISPR/Cas induced mutants in rice

Detection of CRISPR-mediated genome modifications through altered methylation patterns of CpG islands (2020) BMC Genomics 21:856. Farris et al made the observation of epigenetic modification provides an indicator that intentionally directed genomic edits can lead to collateral, unintentional epigenomic changes post modification with generational persistence.

Assessing the risks of topically applied dsRNA-Based products to Non-Target Arthropods. (2020) Romeis J., and Winmer F, Front. Plant Sci. 11:679. Arthropods form an important part of the biodiversity in agricultural landscapes and contribute important ecosystem services. The report studies the adverse environmental effects from the use of dsRNA on valued non-target species, Arthropods.

Broadening the GMO risk assessment in the EU for genome editing technologies in agriculture (2020) Kawall K, Cotter J, Then C discuss the problems with GE and the need for regulators to have the best detection and assessment tools for them.

A Real-Time Quantitative PCR Method Specific for Detection and Quantification of the First Commercialized Genome-Edited Plan. (2020) Foods, Chhalliyil, P., et al Foods, 9(9), p.1245. New development test for gene edited GMO's.

Update correction (2022) A real time PCR quantitive method.

Genome Editing in Food and Farming — Risks and unexpected consequences, (2020) Dr. Janet Cotter (LE), Dana Perls (FOE), review assistance from Dr. Jonathan Latham (BRP). A report on genome editing and how it can create genetic errors, such as “off-target” and “on-target” effects, leading to unexpected and unpredictable outcomes in the resulting GMO.

Repair of double-strand breaks induced by CRISPR–Cas9 leads to large deletions and complex rearrangements (2019) Kosicki et al report significant on-target mutagenesis, such as large deletions and more complex genomic rearrangements at the targeted sites in mouse embryonic stem cells, mouse hematopoietic progenitors and a human differentiated cell line.

Search-and-replace genome editing without double-strand breaks or donor DNA. Nature(2019), A.V., Randolph, P.B., Davis, J.R. et al. dos:10.1038/s41586-019-1711-4. Prime editing offers a better efficiency... and much lower off-target editing than Cas9 nuclease at known Cas9 off-target sites. (Abstract)

A rapid method for detection of mutations induced by CRISPR/Cas9-based genome editing in common wheat (2019) Plant Biotechnology, Kamiya Y et al results show that frequencies of mutations tended to be higher in gene edited wheat than in the plants transformed by Agrobacterium. This method of rapid detection of edited mutations could be used for variety of applications, such as screening of target sequences or modified vectors for efficient CRISPR/Cas9 genome editing in wheat.

Genetically Engineered Animals: From Lab to Factory Farm (2019) Friends of the Earth report provides insight on health, environmental, ethical and consumer concerns raised by research on genetically engineered animals.

Transgenic Aedes aegypti Mosquitoes Transfer Genes into a Natural Population (2019) Scientific Reports Evans BR., et al report on new strain of fertile GE hybrid mosquito offspring sufficiently robust to be able to reproduce in nature. (criticisms lodged)

Genetically engineered hornless cattle: flaws in the genome overlooked. Test Biotech (2019) report on risks overlooked due to screening errors.

GENE DRIVES A report on their science, applications, social aspects, ethics and regulations. (2019) The European Network of Scientists for Social and Environmental Responsibility (ENSSER) report into gene drive organisms (GDO) and the public and scientific issues that need to be addressed before any GDOs are released.

Promises and perils of gene drives: Navigating the communication of complex, post-normal science. Proceedings Of The National Academy Of Sciences, 116(16), 7692-7697. Brossard, D., Bullock, P., Gould, F., & Wirz, C. (2019) discuss the roles of public opinion in public engagement with scientific processes on issues such as gene drives.

A large-scale whole-genome sequencing analysis reveals highly specific genome editing by both Cas9 and Cpf1 (Cas12a) nucleases in rice. (2018) Genome Biology 19:84. Tang et al results clearly show that most mutations in edited plants are created by the tissue culture process, which causes approximately 102 to 148 single nucleotide variations (SNVs) and approximately 32 to 83 insertions/deletions (indwells) per plant.

Forcing The Farm: (2018) ETC Group, How Gene Drive Organisms Could Entrench Industrial Agriculture and Threaten Food Sovereignty.

A CRISPR–Cas9 gene drive targeting doubles causes complete population suppression in caged Anopheles gambiae mosquitoes. Nat. Biotechnol. (2018) Kyrou K, et al study found A CRISPR–Cas9 gene drive construct spread rapidly in caged mosquitoes, reaching 100% prevalence within 7–11 generations (population collapse)...We note that these proof-of-principle experiments cannot conclude that this drive is resistance proof.

Inter-homologue repair in fertilized human eggs? (2018) Nature: 560,E5–E7. Eli D., et al found that CRISPA/Cas9 has the potential to reduce disease-causing alleles, but inadvertent changes to the human germ line, including rearrangements, long deletions, and loss of heterozygosity,could have serious consequences that affect development, predisposition to cancer and fertility.

Repair of double-strand breaks induced by CRISPR–Cas9 leads to large deletions and complex rearrangements(2018). Nature Biotechnology. pp.1-7. Kosicki M., et al summarized '"¦ we show that DNA breaks introduced by single-guide RNA/Cas9 frequently resolved into deletions extending over many kilobases. Furthermore, lesions distal to the cut site and crossover events were identified. The observed genomic damage in mitotically active cells caused by CRISPR–Cas9 editing may have pathogenic consequences.

Evolution of Resistance Against CRISPR/Cas9 Gene Drive. (2017) Genetics 205(2):827–841. Unkless, Clark and Messer (2017) showed that resistance to standard CRISPR/Cas9 gene drive (CGD) approaches should evolve almost inevitably in most natural populations... The key factor determining the probability that resistance evolves is the overall rate at which resistance alleles arise at the population level by mutation or nonhomologous end joining (NHEJ).

In silico identification of off-target pesticidal dsRNA binding in honey bees (Apis mellifera) (2017) PeerJ, Mogren C., Lundgren J. research identified 101 insecticidal RNAs sharing high sequence similarity with genomic regions in honey bees that pose off target effects

The Democratization of Gene Editing: Insights from site-specific cleavage and double-strand break repair, (2016) DNA Repair (Amst), Jansin M., and Haber J E. report on the site specific dangers of DSB repair mechanisms and site-specific cleavage systems.

Mechanisms and Consequences of Double-strand DNA Break Formation in Chromatin (2016) J.Cell Physiology, Cannan W.J and Pederson D.S. outline the mutagenic effects to the chromosomes from double stranded breaks in DNA.

CRISPR/Cas9 systems targeting β-globin and CCR5 genes have substantial off-target activity. (2013) Nucleic Acids Research, 41 (20), 9584-9592. Cradick, Fine, Antico & Bao, found that the repair of the on-and off-target cleavage resulted in a wide variety of insertions, deletions and point mutations