Study finds CRISPR causes ‘catastrophic’ DNA damage in plants

TWN Info Service on Biosafety
16 August 2023
Third World Network


Dear Friends and Colleagues

Study finds CRISPR causes ‘catastrophic’ DNA damage in plants

CRISPR genome editing techniques induced ‘catastrophic’ DNA damage, including whole chromosomal loss and other unintended changes such as large-scale deletions, rearrangements and translocations and micronuclei formation in tomatoes (Item 1). This is the first study to document such chromothripsis-like events in plants following genome editing, which has already been documented in animal and human cells.

These findings are the latest to challenge the notion that CRISPR and other genome editing techniques are ‘precise’ and thus safe. The genetic damage associated with CRISPR appears to be an inherent risk of the editing technology, due to the manner by which CRISPR systems induce genetic changes, warranting regulations that allow for safety assessments to be performed to rule out such unintended effects that may have implications for food and environmental safety, as well as for agronomic performance.

As explained by Testbiotech’s backgrounder (Item 2), standard CRISPR systems begin the process of editing DNA by inducing double-stranded breaks in DNA. The next stage of the editing process then relies on the cell to repair the broken DNA, a process not controlled by developers. Rather than these broken double strands repairing in the manner that generates the genetic changes desired by the developer, the cell may attempt to patch up the broken DNA in detrimental ways, resulting in widespread genetic and chromosomal damage.

The issue of CRISPR-associated incorrect DNA repair is uncontested in the medical field where genome editing is researched for medical interventions, and for which standards of safety and precaution are higher than in the agritech field. DNA repair processes, including aberrant repair, is less understood in plants. This study is thus important in documenting the first cases of chromothripsis-like events in plants and builds on previous findings of other forms of DNA disrepair in plants following genome editing.

With best wishes,
Third World Network

Item 1
A CRISPR-induced DNA break can trigger crossover, chromosomal loss and chromothripsis-like rearrangements
Samach A, et al. (2023). BioRxiv, 24 May 2023.


The fate of DNA double-strand breaks (DSBs) generated by the Cas9 nuclease has been thoroughly studied. Repair via non-homologous end-joining (NHEJ) or homologous recombination (HR) is the common outcome. However, little is known about unrepaired DSBs and the type of damage they can trigger in plants. In this work, we designed a new assay that detects loss of heterozygosity (LOH) in somatic cells, enabling the study of a broad range of DSB-induced genomic events. The system relies on a mapped phenotypic marker which produces a light purple color (Betalain pigment) in all plant tissues. Plants with sectors lacking the Betalain marker upon DSB induction between the marker and the centromere were tested for LOH events. Using this assay we detected a flower with a twin yellow and dark purple sector, corresponding to a germinally transmitted somatic crossover event. We also identified instances of small deletions of genomic regions spanning the T-DNA and whole chromosome loss. In addition, we show that major chromosomal rearrangements including loss of large fragments, inversions, and translocations were clearly associated with the CRISPR-induced DSB. Detailed characterization of complex rearrangements by whole genome sequencing, molecular, and cytological analyses, supports a model in which breakage-fusion-bridge cycle followed by chromothripsis-like rearrangements had been induced. Our LOH assay provides a new tool for precise breeding via targeted crossover detection. It also uncovers CRISPR mediated chromothripsis-lke events that had not been previously identified in plants.


Item 2

CRISPRthripsis in plants
Gene scissors found to cause chaos in the genome of tomatoes

20 June 2023 / Recent scientific findings have revealed chromothripsis-like effects after the application of CRISPR/Cas in the genome of tomatoes. Chromothripsis refers to a phenomenon in which often several hundred genetic changes occur simultaneously in a ‘catastrophic’ event. Many sections of the genetic material can be swapped, twisted, recombined or even lost if this occurs.

It has been known for some time that ‘CRISPRthripsis’, which is another term for the above-described phenomenon, occurs in mammalian (and human) cells. This effect has now been also demonstrated in plants after gene scissor applications. The new study was already published before the peer-review process. The findings show that gene scissor applications cause unintended genetic alterations much more frequently than previously thought, affecting large parts of the genome.

When both strands of DNA are cut, as is typically the case with the CRISPR/Cas, the ends of the chromosomes can loose contact with each other. If the repair of the break in the chromosomes fails, the severed ends can be lost, restructured or incorporated elsewhere. Chromothripsis otherwise seems to be relatively rare in plants. CRISPR/Cas applications can frequently result also in changes at genomic sites that are particularly well-protected by natural repair mechanisms. The risks cannot generally be estimated, they must be investigated thoroughly in each and every case.

The recent findings shed new light on the alleged ‘precision’ of gene scissors: although the new technology can be used to target and cut precise locations in the genome, the consequences of ‘cutting’ the genome are to some extent unpredictable and uncontrollable. Plants obtained from new genetic engineering (New GE) cannot, therefore, be regarded as safe per se, and need to be thoroughly investigated for risks.

Without exact genomic analyses, chromothripsis can be easily overlooked. It is, for example, not unlikely that it also occurred in plants obtained from New GE that were already deregulated in the US.

Attempts are currently being made in Europe to largely deregulate plants obtained from CRISPR/Cas applications. According to leaked documents, the EU Commission plans to give companies permission to release New GE plants into the environment and to market their products after only a short period of notification. Similar to the USA, the proposed criteria exempting them from mandatory risk assessment would not require any investigation of unintended genetic changes, e. g. chromothripsis. The new regulation would not only be applicable to plants used in agriculture, but also would allow the release of wild plants with no in-depth risk assessment. Testbiotech is warning that the planned deregulation and large scale releases of New GE organisms could threaten natural resources needed by future generations.

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