Integration Site Selection by Retroviral Vectors: Molecular Mechanism and Clinical Consequences

Retroviral DNA integration into the host cell genome is an essential feature of the retroviral life cycle. The ability to integrate their DNA into the DNA of infected cells also makes retroviruses attractive vectors for delivery of therapeutic genes into the genome of cells carrying adverse mutations in their cellular DNA. Sequencing of the entire human genome has enabled identification of integration site preferences of both replication-competent retroviruses and retroviral vectors. These results, together with the unfortunate outcome of a gene therapy trial, in which integration of a retroviral vector in the vicinity of a protooncogene was associated with the development of leukemia, have stimulated efforts to elucidate the molecular mechanism underlying integration site selection by retroviral vectors, as well as the development of methods to direct integration to specific DNA sequences and chromosomal regions. This review outlines our current knowledge of the mechanism of integration site selection by retroviruses in vitro, in cultured cells, and in vivo; the outcome of several of the more recent gene therapy trials, which employed these vectors; and the efforts of several laboratories to develop vectors that integrate at predetermined sites in the human genome

Enterotypes in the landscape of gut microbial community composition

Population stratification is a useful approach for a better understanding of complex biological problems in human health and wellbeing. The proposal that such stratification applies to the human gut microbiome, in the form of distinct community composition types termed enterotypes, has been met with both excitement and controversy. In view of accumulated data and re-analyses since the original work, we revisit the concept of enterotypes, discuss different methods of dividing up the landscape of possible microbiome configurations, and put these concepts into functional, ecological and medical contexts. As enterotypes are of use in describing the gut microbial community landscape and may become relevant in clinical practice, we aim to reconcile differing views and encourage a balanced application of the concept

Transposable elements as plasmid-based vectors for long-term gene transfer into tumors

A primary limitation to using nonviral vectors for cancer gene therapy is transient expression of the therapeutic gene. Even when the ultimate goal is tumor cell death, a minimum threshold of gene expression is required to kill tumor cells by direct or indirect mechanisms. It has been shown that transposable elements can significantly enhance the duration of gene expression when plasmid DNA vectors are used to transfect tumor or tumor-associated stroma. Much like a retrovirus, transposon-based plasmid vectors achieve integration into the genome, and thereby sustain transgene expression, which is especially important in actively mitotic cells such as tumor cells. Herein we briefly discuss the different transposons available for gene therapy applications, and provide a detailed protocol for nonviral transposon-based gene delivery to solid experimental tumors in mice