Science in Society Archive

Scrambled genomes in human gene therapy and transgenic plants

Introducing foreign DNA into human or plant genomes both lead to genome scrambling. Prof. Joe Cummins and Dr. Mae-Wan Ho review the latest evidence.

Human gene therapy is usually considered separate and distinct from genetic modification (GM) of crops. Adeno-associated virus vectors (AAV) are most commonly used in clinical gene-therapy trials.

The wild-type adenovirus has terminal repeats that enable it to integrate into human chromosome 19 at a specific site. The AAV vector, however, has no specific integration site. It often integrates into chromosome 19, though not at the integration site of the wild-type virus, and it may also integrate into any of the other human chromosomes. AAV vector is preferred for most gene therapy experiments because the chromosome insertion is more stable and the AAV vector transforms both dividing and non-dividing cells.

Crop GM is achieved using Agrobacterium transformation or direct plasmid transfer using biolistic transformation (gene gun) methods. The Agrobacterium T -DNA vector is flanked by 25 base-pair direct repeats that facilitate integration of plasmid sequences into the plant chromosome.

The common features of gene therapy in human cells and crop GM is the presence of integrating vector sequences flanking transgene(s) each equipped with a promoter to drive expression.

While many studies have been carried out on transgenic DNA in plants, there have been relatively few that analysed host genome at the site of insertion. In a recent issue of Nature Genetics, researchers in the Department of Medicine, University of Washington Seattle, report that integrated proviruses are "associated with chromosomal deletions and other rearrangements and are frequently located on chromosome 19 (although not at the wildtype AAV integration site)" [1].

The researchers analysed the chromosomal DNA flanking the site of vector insertion. By searching the human genome sequence databases, the junctions were located to 6 different chromosomes. Four integrated into genes, one in an exon (a coding module of the gene). None of the sites of insertion showed significant DNA base sequence homology to the AAV vector or to each other. Four of the 9 provirus (the inserted vector) had junctions within a relatively large, 22-Mb (millions of base pairs) region of chromosome 19 (19q13), but not the wild type site, which only spans 1kb.

Chromosomal deletions of 9 to 71 bps were found at the site of five insertions, sometimes associated with additions of 1 to 13 bp (base pairs) of uncertain origin. In one site, a translocation (movement of DNA) between chromosomes 7 and 19 had occurred, with AAV vector sequences between them. Another contained a translocation or a deletion of more than 258 bp. There were also unexpected vector sequences at integration sites. In one site, one ITR (inverted terminal repeat) was linked to 875 bp of the plasmid used to carry vector during preparation.

The authors state, "these findings, as well as the ITR deletions and other vector genome modifications noted previously, demonstrate the imprecision and variability of AAV vector packaging and integration".

The study is reminiscent of the recent finding of unexpected sequences and genome scrambling associated with transgenes in GM crops such as soybean [2]. Further analysis is likely to show that scrambled and unexpected sequences are commonplace in GM crops, and that they arise by non-homologous recombination at double strand DNA breaks. We have questioned the legality and safety of approving crops that contain unknown, uncharacterised DNA sequences [3]. If these are found even in the most widely distributed and established commercial GM crop, the problems are likely to be worse with newer transgenic crops of corn, cotton or canola, which have yet to be analysed [4]. Certainly, government regulators and their academic satellites seem passive and submissive in dealing with important findings that question the safety of GM crops.

The observation that gene scrambling occurs in both human gene therapy and in GM crops suggest that there is a fundamental flaw in both genetic engineering technology and in the auditing of molecular properties of the modified humans or crops.

The corporate audit of molecular characteristics in gene therapy vectors and those of GM crops may be analogous to the Enron audits of the Arthur Anderson Accounting Firm. Those outside of direct involvement in gene therapy and crop genetic modification should be well enough informed to require full and truthful molecular audits of gene therapy vectors and GM crops.

Article first published 07/03/02


  1. Miller D, Rutledge A and Russell D. "Chromosomal effects of adeno-associated virus integration"2002 Nature genetics 30,147-8
  2. Windels P, Taverniers I, Depicker A, Van Bockstaele E and De Loose M (2001). Characterisation of the Roundup Ready soybean insert. Eur Food Res Technol DOI 10.1007/s002170100336, © Springer-Verlag.
  3. Ho M and Cummins J "Europe to Demand Strict Molecular Characterisation for GMOs?" ISIS Press Release - May 21 2001
  4. Cummins J "GM Crops May All Be Unstable" ISIS Report April 8, 2001

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