Proteomics characterization of the adenovirus VA1 non-coding RNA on the landscape of cellular proteome

Abstract

Abstract Objectives Gene therapy using adenoviruses has shown tremendous promise in animal and human models in the past. The tumor responses achieved by these viruses were either because of their oncolytic properties or therapeutic genes expressed from the genome of the virus. We have previously shown enhanced viral replication in cell models that have lost or lower expression of the cyclin dependent kinases inhibitor (p21/Waf-1). Beside the early onset of many viral genes in the p21/Waf-1 knock out cell model, we observed a significantly higher copy number for the viral VA1 but non VA2 non-coding RNA transcripts. In this study we investigated the effect of adenoviral VA1 non-coding RNA on the landscape of cellular proteins. Methods Using a DU145 cell line as a model that was transiently transfected with a plasmid carrying the adenoviral VA1 non-coding RNA, we were able to study changes in the proteome and the cellular cascade of the cells. Using state of the art global proteomics analyses of the differentially expressed proteins between the VA1 overexpressed and control cells demonstrated how the early onset of VA1 transcript affected cellular machinery. Results Using a 1.5 fold cut off between the down-regulated or overexpressing proteins, we were able to demonstrate how the non-coding VA1 gene might be responsible for suppressing the proteasome degradation, the endocytic and lysosomal pathways. Similarly, overexpression of the non-coding VA1 transcript was responsible for the upregulation (1.5 fold) of approximately 40 different proteins in the spliceosome machinery. Conclusions These data demonstrated how the non-coding VA1 RNA functioned independently of any other viral proteins in modulating the cell signaling cascades to promote viral propagation. To our knowledge this is the first report to investigate the function of VA1 non-coding RNA on the cellular proteome.