Analysis of Adenovirus-Host Interactions to Improve Adenoviral Vectors for Gene Therapy

....................................................................................................................... 1 Introduction ............................................................................................................1 1.1 Adenoviral Vectors ...................................................................................................2 1.1.1 Adenovirus taxonomy and virus particle composition...........................................2 1.1.2 Infection and replication cycle of adenoviruses ....................................................4 1.1.3 Types of recombinant adenoviral vectors and their application in gene therapy..5 1.1.4 Adenoviral vector modifications............................................................................9 1.2 RNA interference.....................................................................................................13 1.2.1 The RNA interference mechanism .....................................................................13 1.2.2 Viral miRNAs and RNAi suppressor proteins .....................................................15 1.2.3 Adenovirus associated RNAs (VA-RNAs) ..........................................................17 1.3 RNAi in gene therapeutic applications .................................................................18 1.4 Aims of the project .................................................................................................22 2 Treatment of HBV infections by shRNAs delivered by an high-capacity adenoviral vector .................................................................................................23 2.1 Materials and Methods ...........................................................................................25 2.1.1 DNA constructs and enzymes ............................................................................25 2.1.2 Cell lines and viruses..........................................................................................26 2.1.3 In vitro studies to characterize efficacy of HC-AdV mediated delivery of shorthairpin RNAs to reduce hepatitis B virus infection..............................................27 2.1.4 Animal studies ....................................................................................................27 2.1.5 Southern Blot analysis to measure HBV genome replication .............................28 2.1.6 Northern Blot to approve processing of short-hairpin RNAs...............................28 2.2 Results .....................................................................................................................29 2.2.1 Cloning of high-capacity adenoviral vectors .......................................................29 2.2.2 Helper virus amplification ...................................................................................30 2.2.3 Large scale production of high-capacity adenoviral vectors in a spinner flask system ................................................................................................................30 2.2.4 Purification of HC-AdV by cesium chloride centrifugation and buffer exchange 32 2.2.5 Titration of HC-AdV by optical density and quantitative Real-Time PCR ...........34