Under almost all conditions using any method, the levels of gene transfer to any cell are low because many barriers exist for the efficient delivery of genes to cells. Taken one step further, gene transfer to tissues within living animals is even worse, at least in part due to these and additional barriers that arise from the architecture of th tissue, mechanical forces within these tissues, and the host's response to exogenous materials. The primary goal of our laboratory is to identify and overcome the intracellular barriers to promote effective gene transfer both in vitro and in vivo. Exogenous DNA, either viral or non-viral, must cross the plasma membrane into the cell, travel through the cytoplasm and the cytoskeletal networks, cross the nuclear envelope, localize to specific regions within the nucleus, and be transcribed in order for gene therapy to be successful. In 2003, we demonstrated that when multiple cell types were exposed to mild equibiaxial stretch, their ability to take up and express foreign DNA was 10-fold more efficient than cells grown under static conditions. We have since shown that such stretch reorganizes the cytoskeleton and concomitantly increases the numbers of stable, acetylated microtubules by inhibiting HDAC6, the major cytoplasmic a-tubulin deacetylase. We exploited this information to improve intracellular DNA movement and transfection efficiency by using pharmacologic inhibitors of HDAC6 in cells and animals. More recently we have focused on how plasmids move along modified and unmodified microtubules for their trafficking to the nucleus during transfection and gene transfer and have identified the constituents of the protein-DNA complexes that form immediately after entry into the cytoplasm and at various times afterward using mass spectrometry and proteomics. Further, by comparing the protein complexes on plasmids that productively traffic through the cell with those on plasmids that do not move, we have been able to identify key proteins that control DNA movement and we hypothesize that modulation of these proteins may be used to further improve gene delivery. Finally, we are also looking at how plasmids traffic once inside the nucleus and have found that plasmids show highly dynamic intranuclear movement that can be used to control gene expression. Plasmids localize to distinct regions within the nucleus based on their sequences and we hypothesize that we can control this movement to optimize gene expression. The experiments in this competitive renewal will dissect pathways used for intracellular trafficking of proteins and DNA-protein complexes in both the cytoplasm and nucleus to enhance gene delivery.
The specific aims are to (1) Determine the role of tubulin acetylation in cytoplasmic trafficking of transfected plasmids;(2) Identify and characterize the composition of the active DNA trafficking complex;and (3) Determine how plasmids move within the nucleus and how this regulates gene expression.

Public Health Relevance

Gene therapy is an exciting and potentially very useful approach to treat a number of diseases at the molecular level. Unfortunately, many barriers for gene delivery to cells and animals exist that must be characterized before they can be overcome, leading to greater levels of gene transfer and gene therapy. Our work has focused on understanding how genes and plasmids move through cells during the gene delivery process and then exploiting our findings to improve gene transfer and gene therapy. We will determine the molecular mechanisms by which DNA moves through the cytoplasm using the cytoskeleton and distributes throughout the nucleus. We will use isolated cell and small animal models along with proteomic, pharmacological, and genetic approaches to answer these questions.

National Institute of Health (NIH)
National Institute of Biomedical Imaging and Bioengineering (NIBIB)
Research Project (R01)
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Gene and Drug Delivery Systems Study Section (GDD)
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Tucker, Jessica
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University of Rochester
Schools of Dentistry
United States
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Badding, M A; Dean, D A (2013) Highly acetylated tubulin permits enhanced interactions with and trafficking of plasmids along microtubules. Gene Ther 20:616-24
Badding, Melissa A; Lapek, John D; Friedman, Alan E et al. (2013) Proteomic and functional analyses of protein-DNA complexes during gene transfer. Mol Ther 21:775-85
Badding, M A; Vaughan, E E; Dean, D A (2012) Transcription factor plasmid binding modulates microtubule interactions and intracellular trafficking during gene transfer. Gene Ther 19:338-46
Badding, M A; Vaughan, E E; Dean, D A (2012) Transcription factor plasmid binding modulates microtubule interactions and intracellular trafficking during gene transfer. Gene Ther 19:354
Eldib, Mootaz; Dean, David A (2011) Cyclic stretch of alveolar epithelial cells alters cytoskeletal micromechanics. Biotechnol Bioeng 108:446-53
Lin, Xin; Dean, David A (2011) Gene therapy for ALI/ARDS. Crit Care Clin 27:705-18
Kaufman, C D; Geiger, R C; Dean, D A (2010) Electroporation- and mechanical ventilation-mediated gene transfer to the lung. Gene Ther 17:1098-104