Captured DNA

November 2019

The pre-eminent biotech breakthrough of the new millennium has undoubtedly been gene-editing.   

For commercial applications, gene-editing is attractive: one, it's simple, two, it's precise in regard to what and where the edit is, three, above all it doesn't insert foreign DNA.  This last attraction is the most important because it's used to claim that gene-edited organisms are non-GM, and that the edits simply mimic what can happen in nature, and that they therefore need no special regulation.  

Apart from number one above, the 'simple' bit, all the rest of these attractions have been proven wrong. 

 

We'ver already heard of the celebrity biotech hornless calves whose genomes turned out to contain the entire bacterial DNA vector used to edit them (and a bit more) [1]. 

Where anyone's taken the trouble to look, gene-edited animal cells in the lab have routinely been found to harbour foreign DNA contamination. By 'foreign' is meant, for example, bovine and goat DNA (including 'jumping' genes) in mouse cells, virus DNA, and quite frequently E.coli (bacterial) DNA. 

Where does all this spurious DNA come from? 

The problem seems to be intrinsic to gene-editing.  All forms of gene-editing use an enzyme which breaks the double DNA 'ladder' leaving four raw 'ends' which strive to repair the rift.  Re-joining may be perfect, or there may be a gain or loss of a little DNA to create a non-functioning ('knock-out') gene.  On the other hand, it may capture any other spare DNA which happens to be in the cell and use this to stick itself back together. 

There are several identified sources of spurious DNA. 

We know, of course, where the E.coli DNA comes from: the gene-editing vector is multiplied up to useable quantities inside E.coli bacteria.  Also, since the vector includes the code for the mechanism which breaks DNA, it could continue to induce further unpredictable DNA captures elsewhere in the cell.   

The source of the viral DNA isn't much of a mystery either, viruses can be found anywhere there are living animal cells. 

The bovine and goat DNA are easy to explain too.  Animal cells won't grow in culture without the growth promoting substances present in animal body fluids.  To make mammalian cells grow, blood fractions from cattle or goats are added to the culture medium.  There could, however, be another source: experiments have shown that tiny membrane-bound bodies created in, and released by, animal cells can contain functional DNA or the related RNA.  These tiny bodies are found in all fluids from living animals, and can be mediators of horizontal gene transfer between unrelated species.

Note. The infamous Chinese scientist who claims to have genetically-edited human babies must have extracted the proteins he used from something living: standard methods involve rabbit or insect cells.

There are solutions to the presence of spurious extra DNA in gene-edited animals.  For example, avoiding the use of sources of DNA contamination such as E.coli, avoiding animal products, and screening all materials used for the presence of virus contamination.  Another solution is to dilute out the DNA contamination by repeated breeding with the original stock, or careful selection of uncontaminated individuals (if any) for further development. 

However, all these remedies present a huge professional effort, they're time-consuming, and costly.  In fact, they nullify all the advantages of speed and ease which are the reason for gene-editing in the first place. 

OUR COMMENT 

There's a huge scope here for disease-causing elements in our livestock, arising from, for example, viruses, susceptibility to diseases linked to the species whose DNA has introgressed, or activated mobile elements ('jumping' genes) in the livestock genome.  And, we can't help wondering what the chances are of DNA in tiny bodies released by the laboratory workers' cells being captured by the genome of the animal cells they're handling? 

Letting Jonathan Latham have the last word: the biotech industry "is not showing much interest in self-examination.  Far greater even than the GMO industry before it, there is a cowboy zeitgeist: blow off problems and rush to market.  Thus most gene-editing companies are reluctant to share information and consequently very little is known about how, in practice, many of these companies derive their 'gene-edited' products."  The findings presented here "provide a compelling case for active government oversight".  "It is not just regulators who need to step up ... Investors, insurers, journalists, everyone (that's you) in fact, should be asking far more questions of the scientists and companies active in gene-editing." 

Background 

[1]  HORNLESS GENE-EDITED COWS WITH EXTRAS - November 2019 

SOURCES: 

• Jonathan Latham, Gene-Editing Unintentionally adds Bovine DNA, Goat DNA, and Bacterial DNA, Mouse Researchers Find, Independent Science News, 23.09.19 
• Ryuichi Ono, et al., 2019, Exosome-mediated horizontal gene transfer occurs in double-strand break repair during genome editing, Nature Communications Biology 
• James R. Edgar, 2016, Q&A: What are exosomes exactly?, BMC Biology-

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