CRISPR catastrophe in the making?

August 2021

 

"CRISPR editing wreaks chromosomal mayhem in human embryos"

(Nature 2.07.20)

"If human embryo editing ... were space flight, the new data are the equivalent of having the rocket explode at the launch pad before take-off"

(University of California genetic engineer, Nature 2.07.20)

"There's no sugar-coating this. This is a restraining order for all genome editors to stay the living daylights away from embryo editing"

(University of California genetic engineer, The Scientist 26.06.20)

More than 10,000 single-gene inherited human disorders have been identified, and genetic engineers have long held a dream of sorting out our defects. Gene editing techniques, such as CRISPR [1], seem like a heaven-sent opportunity to tweak these dysfunctional genes back to normality.

In 2017, a paper was published describing a promising, efficient, accurate and safe method for editing heritable mutations in human embryos. The study concluded that the embryonic cells they had edited had spurned the artificial DNA offered and apparently used the DNA sequence from the healthy parent as a template to correct themselves after CRISPR had cut their faulty gene.

Since Big Biotech, patents and profits weren't involved, and no one was trying to destroy anyone else's reputation or to muddle the science, what followed was a gentlemanly discussion in the scientific press.

Other researchers in the field pointed out that, due to the limitations of DNA analysis (you've got to know what you're looking for before you can find it), CRISPR may simply have wrecked the chromosome instead of correcting it, leaving only the DNA from the healthy parent 'visible' to the science. They also pointed out that the CRISPR editor was introduced before the maternal and paternal chromosomes (the DNA-carrying structures) came together, leaving no physical opportunity for the suggested template-based correction to happen.

The authors then did what scientists do (more research), and published further results supporting their previous conclusion.

This seems like a good start on the path to successfully correcting faulty human genomes using CRISPR. However, the scientists' discussion revealed some limitations and findings which are less encouraging.

Because the embryos have to be tested at a very early stage to see if they have been successfully edited, very little DNA is available for testing and assays may be unreliable.

The DNA 'correction' arising when the healthy parent sequence is used as a template doesn't just sort out the little bit of DNA cut by CRISPR, but extends a long way in both directions around the original faulty target site. This heralds a loss of genomic diversity, which is a serious safety issue as it can lead to disease in the offspring.

It's interesting that, besides the signs that cells have the intelligence not to use man-made DNA when a natural alternative presents itself, this suggests the cell is intelligent enough to know there will be extensive disruption to adjacent DNA around the single break and that these sequences must, therefore, be 'corrected' too.

There's mounting evidence that pairs of chromosomes interact with each other, particularly in regard to vital repair processes.

This essential, protective, chromosome-based repair mechanism could be permanently disrupted by any kind of artificial genetic modification in animals or plants with dire long-term consequences.

Most concerning is the revelation that CRISPR injected into the reproductive cell of one parent so as to correct an inherited DNA error there, actually continues to be active after the maternal and paternal cells have come together.

With this comes the possibility that CRISPR could find DNA to chop and change, not only as intended, but all over the genomes passed down from both parents.

Fast forward to 2020. More refined techniques, more penetrating investigations, and a diversity of experimental materials have generated a stream of papers on CRISPR gene editing in human embryos (see [2] plus SOURCES).

These reveal genome damage ranging from subtle mutations around the immediate DNA site targeted for repair, to pervasive off-target nicks in one strand of the DNA 'ladder', to 'edited' genomes in which half the CRISPR-induced DNA breaks remained unrepaired, to chromosome rearrangements or complete loss. The previously questioned use of the healthy chromosome to guide the repair was, however, widely reported.

Some authors commented on the possibility that successful gene editing could be hindered by, for example, structural aspects of the chromosome, cell cycle effects, and epigenetic aspects. One author warns "Our results serve as a cautionary note for the use of induced double-strand breaks in editing the genome of human embryos for clinical use. Chromosomal material may be lost and result in developmental abnormalities ...", and note that our understanding of the significance of epigenetic effects in GM animals and plants is very much in its infancy [3,4].

All these 'CRISPR-induced disruptions found in human embryos will also be happening in gene-edited plants along with the increased risk of plant disease, ecosystem disruption, and harm to consumers. Very few studies have been carried out on gene-edited plants: the parties planning to gain from them don't want know about any problems. However, a recent study of gene-edited rice did, indeed, find a wide range of undesirable and unintended on- and off-target mutations. There was a clear lack of precision in the outcome, and the hoped-for yield increase in the rice turned out to be a decrease.

OUR COMMENT

This year's gene-edited dream sounds like next year's nightmare.

The Government in Westminster seems to have little appetite to grapple with the inherent problems of GM any any form [5]. In the case of creating GM humans there are, at least, ethical checks in the system: where GM plants are concerned, our regulators seem to have their minds so focused on the commercial potential that the warnings and paucity of the science are blotted out. It seems the Government in Holyrood isn't any different.

Try to bring all these gene-editing side-effects and deficiencies to your regulators' attention. You can contact your MP and MSP using www.writetothem.com.


Background

[1] CRISPR/Cas9 GENE EDITING - March 2016

[2] CRISPR KNOCK-OUT OR KNOCK-ON - March 2020

[3] AVOIDING UNWANTED GENETIC BAGGAGE - April 2019

[4] CRISPR'S EPIGENETIC SCARS - August 2021

[5] THE PRECISION PROBLEM IN GENOME EDITING - August 2021


SOURCES:

• Hong Ma, et al., August 2017, Correction of a pathogenic gene mutation in human embryos, Nature 413

• Dieter Egli, et al., August 2018, Inter-homologue repair in fertilized human eggs? Brief Communications Arising, Nature 560

• Fatwa Adikusuma, et al., August 2018, Large deletions induced by Cas9 cleavage, Brief Communications Arising, Nature 560

• Hong Ma, et al., August 2018, Ma et al. reply, Brief Communications Arising, Nature 560

• Brett M. Sansbury, et al., 2019, Understanding the diversity of genetic outcomes from CRISPR-Cas generated homology-directed repair, Biology Communications, Nature 2:458

• Amanda Heidt, CRISPR Gene Editing Prompts Chaos in DNA of Human Embryos, The Scientist, 26.06.20

• Heidi Ledford, CRISPR editing wreaks chromosomal mayhem in human embryos

• New tool for rapidly analysing CRISPR edits reveals frequent unintended edits, GM Watch, 6.01.20

• Micheal V. Zuccaro, Reading frame restoration at the EYS locus, and allele-specific chromosome removal after Cas9 cleavage in human embryos, Cold Spring Harber Laboratory Preprint 18.06.20

• Gregorio Alanis-Lobato, et al., Frequent loss-of-heterozygosity in CIRSPR-Cas9-edited early human embryos, bioRxiv Preprint 5.06.20

• Karthik Murugan, et al., CRISPR-Cas12a has widespread off-target and dsDNA-nicking effects, Journal of Biological Chemistry Papers in Press 11.03.20

• Scientists "surprised" to find that CRISPR editing tool is not as precise as previously claimed, GM Watch 2.04.20

• Dan Liang, et al., Frequent gene conversion in human embryos induced by double strand breaks, bioRxiv Preprint, 20.06.20

• CRISPR gene editing in human embryos "wreaks chromosomal mayhem" - Nature journal, GM Watch, 6.07.20

• CRISPR-edited rice shows wide range of unintended mutations, GM Watch, 9.06.20

• Sukumar Biswas, et al., Investigation of CRISPR/Cas9-induced SD1 rice mutants highlights the importance of molecular characterization in plant molecular breeding, Journal of Genetics and Genomics Pre-proof accepted 1.04.20