Gene therapy from the perspective of systems biology

Gene therapy research has expanded from its original concept of replacing absent or defective DNA with functional DNA to include the manipulation (increase or decrease) of gene expression by the delivery of modified genes, siRNA or other genetic material via multiple vectors, including naked plasmid DNA, viruses and even cells. Specific tissues or cell types are targeted in order to decrease the risks of systemic or side effects. As with the development of any drug, there is an amount of empiricism in the choice of gene target, route of administration, dosing and, in particular, the scaling-up from preclinical models to clinical trials. High-throughput experimental and computational systems biology studies that account for the complexities of host-disease-therapy interactions hold significant promise in assisting in the development and optimization of gene therapies, including personalized therapies and the identification of biomarkers to evaluate the success of such strategies. This review describes some of the obstacles and successes in gene therapy, using the specific example of growth factor gene delivery to promote angiogenesis and blood vessel remodeling in ischemic diseases; anti-angiogenic gene therapy in cancer is also discussed. In addition, the opportunities for systems biology and in silico modeling to improve on current outcomes are highlighted.