Experimental evidence for a novel mechanism of transposition – Vector choice and gene transfer

Due to their numbers and mobility, transposable elements (jumping genes) have been playing an important role in genome evolution. There are two major classes of transposable elements: DNA transposons that move through a non-replicative mechanism, and retrotransposons that generate copies of themselves and move by a replicative mechanism. Around the turn of the century, a new group of transposons were postulated, the Helitron elements, which were proposed to represent the first replicative DNA transposons in eukaryotes. However, not a single transpositionally active Helitron transposon has yet been isolated.

The research group of Dr. Zoltan Ivics, head of the Division of Medical Biotechnology, in collaboration with scientists at the Max Delbrueck Center for Molecular Medicine in Berlin and with other international collaborators, used molecular biology methods to reconstruct Helraiser, an ancient Helitron transposon in the bat genome. The scientists used this transposon as a model to study the transposition mechanism of Helitrons in the genome. They established a novel mechanism of genome shuffling, during which the transposon picks up and carries host cell DNA over to new genomic locations [1]. Ivics and his colleagues believe that the unique features of Helraiser could be exploited for the purpose of gene transfer. For example, the genome shuffling feature could be utilized to distribute transcriptional regulatory signals in the genome of cell-based models. Moreover, the scientists showed that a covalently closed circular form of the transposon acts as an intermediate molecule during transposition, suggesting a replicative process. This feature would be highly useful for the generation of cell-based models where multiple copies of a transgene are required.

The utility of Sleeping Beauty, an engineered transposon reconstructed from >10 million-year-old elements found in fish genomes, has been previously highlighted by Ivics and his collaborators. For example, the Sleeping Beauty transposon is highly efficient to move gene constructs into the germline of experimental animals [3-5], and this can be useful for the generation of animal models for preclinical drug testing.

Vector choice and the safety of gene transfer

Another research focus of Ivics and his colleagues is the potential risks of gene vector integration in the context of gene therapy. As gene transfer tools, among other systems, vectors derived from the Mouse Leukemia Virus (MLV), the HIV lentivirus and transposons can be used. Ivics and his collaborators compared the genome-wide distribution of insertion sites of the Sleeping Beauty and piggyBac transposons and the MLV and HIV retroviral vectors in a certain type of cell of the human immune system, the CD4+ T cells [2]. The scientists found that the Sleeping Beauty transposon has the highest chance of integrating into safe genomic sites (so called „safe harbor“ sites). In contrast, the highly similar insertion profiles of the MLV retrovirus and the piggyBac transposon showed that they are often inserted in genomic regions where the integration of a gene construct could carry a risk. Indeed, the scientists found markedly different frequencies of the four vector systems to target genes, whose deregulation was previously found to be associated with severe adverse events in gene therapy clinical trials. „Our data underscore the importance of vector choice for therapeutic gene transfer to minimize potential mutagenic effects on cells, and suggest that Sleeping Beauty could have an advantage in this respect in comparison with some other vector systems“ – explains Ivics.

Original Publications

1. Grabundzija I, Messing SA, Thomas J, Cosby RL, Bilic I, Miskey C, Gogol-Döring A, Kapitonov V, Gerhardt DJ, Diem T, Dalda A, Jurka J, Pritham EJ, Dyda F, Izsvák Z, Ivics Z (2016): A Helitron Transposon Resurrected From the Bat Genome Reveals a Novel Mechanism of Genome Shuffling in Eukaryotes.
Nat Commun Mar 2 .
DOI 10.1038/NCOMMS10716

2. Gogol-Döring A, Ammar I, Gupta S, Bunse M, Miskey C, Chen W, Uckert W, Schulz TF, Izsvák Z, Ivics Z (2016): Genome-Wide Profiling Reveals Remarkable Parallels Between Insertion Site Selection Properties of the MLV Retrovirus and the piggyBac Transposon in Primary Human CD4+ T Cells.
Mol Ther Jan 12 .
DOI: 10.1038/mt.2016.11

3. Ivics Z, Garrels W, Mátés L, Yau TY, Bashir S, Zidek V, Landa V, Geurts A, Pravenec M, Rülicke T, Kues WA, Izsvák Z (2014): Germline transgenesis in pigs by cytoplasmic microinjection of Sleeping Beauty transposons.
Nat Protoc 9: 810-827.

4. Ivics Z, Hiripi L, Hoffmann OI, Mátés L, Yau TY, Bashir S, Zidek V, Landa V, Geurts A, Pravenec M, Rülicke T, Bösze Z, Izsvák Z (2014): Germline transgenesis in rabbits by pronuclear microinjection of Sleeping Beauty transposons.
Nat Protoc 9: 794-809.

Online-Abstract

5. Ivics Z, Mátés L, Yau TY, Landa V, Zidek V, Bashir S, Hoffmann OI, Hiripi L, Garrels W, Kues WA, Bösze Z, Geurts A, Pravenec M, Rülicke T, Izsvák Z (2014): Germline transgenesis in rodents by pronuclear microinjection of Sleeping Beauty transposons.
Nat Protoc 9: 773-793.

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The Paul-Ehrlich-Institut, the Federal Institute for Vaccines and Biomedicines, in Langen near Frankfurt/Main is a senior federal authority reporting to the Federal Ministry of Health (Bundesministerium für Gesundheit, BMG). It is responsible for the research, assessment, and marketing authorisation of biomedicines for human use and immunological veterinary medicinal products. Its remit also includes the authorisation of clinical trials and pharmacovigilance, i.e. recording and evaluation of potential adverse effects.

Other duties of the institute include official batch control, scientific advice and inspections. In-house experimental research in the field of biomedicines and life science form an indispensable basis for the manifold tasks performed at the institute.

The Paul-Ehrlich-Institut, with its roughly 800 members of staff, also has advisory functions nationally (federal government, federal states (Länder)), and internationally (World Health Organisation, European Medicines Agency, European Commission, Council of Europe etc.).

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