Host cell gene and pathway changes associated with high baculovirus in vitro production yields

Baculovirus-insect cell culture technology is applied for the production of veterinary and human vaccines‚ gene delivery vectors‚ and biopesticides. The current study investigated systemic cell – virus interactions under different cell culture conditions resulting in differing in virus occlusion bodies (OB)/cell yields for HearNPV infected Hzea cells. 22 microarrays were used. While mRNA levels for most genes decreased, a core set of 14 genes consistently increased in all 11 different infection conditions studied‚ suggesting a conserved up regulation pattern of these genes upon baculovirus infections. KEGG pathway analysis found strongest responses by the genes for the E3 ubiquitin-protein ligase Topors in the ubiquitin proteasome pathway‚ GAPDH in the glycolytic pathway‚ and host DNA ligase and DNA helicase in the replication process. Weighted co expression network analysis determined a module and 5 hub genes that strongly correlated to OB/cell yields. The endoplasmic reticulum functional group was particularly reduced in low producing systems. Total virus mRNA and viral genome levels had positive correlations to OB/cell yields. Virus genes were expressed in a similar temporal pattern regardless of the cell lines‚ media or infection cell densityies used. The virus Chitinase gene and Superoxide dismutase gene may be particularly important for high productivities. Overall this genome-scale expression study of different infection conditions provides insights into host insect cell responses to baculovirus infections and suggests gene expression changes that are likely important for high virus yields. To investigate host insect gene responses to baculovirus infection under different conditions, a set of custom microarray probes, based on de novo assembly of target sequences from deep transcriptome sequencing (SRA048534; GEO accession number: GSE34418), were used to simultaneously investigate expression of 8760 Helicoverpa zea insect genes and 134 H. armigera nucleopolyhedrovirus (HearNPV, Accession: NC_002654)) genes. In this study‚ 22 Agilent arrays (from 3 slides of 8x15,000 SurePrint Agilent format) were used to analyze samples from: 4 infections of a so called good clone generating high OB yields (duplicate cultures at 0 hour before infection (h.b.i) and at 18 h.p.i)) and 4 corresponding infections of a bad clone (poor OB yields); 6 infections of cells grown in different media (Sf900III plus FBS, IPL plus YL, and Grace's plus FBS) and 8 samples of infections conducted at low vs. high cell densities in SF900III medium, (2 replicates for each time-point‚ 0 h.p.i and 18 h.p.i‚ and for cell densities 5x10^5 and 2x10^6 cells/ml).