Retrovirus derived particles found valuable biotechnological application in Vaccinology and Gene
therapy, although challenging from the manufacturing view-point, due to the low titers and high content of
contaminant defective particles. Additionally, retroviruses such as HIV are a major world-wide health
concern with the cell-virus interaction dynamics poorly understood. Thus, an integrated overview on the
cellular determinants of retrovirus production in human cells can provide a valuable starting point and a
potential tool to address these and other issues.
In this work, we analyzed transcriptome changes between retrovirus producers and the corresponding
parental cells using two different human cell lines, and took a pathway analysis approach to identify
biochemical networks overrepresented in the virus production state. Nearly 200 pathways were identified,
majorly represented by signaling and metabolism. Retrovirus production induced transcriptome changes
associated with apoptotic and cell survival pathways suggesting a balance between both networks, a typical
feature of virus infection scenario. Fatty acid metabolism was among the most prominently up regulated
pathways, along with sphingolipid and phospholipid metabolism, suggesting increased membrane recycling
dynamics for viral replication. Amino acid degradation was notably up-regulated as well. Virus production
appears to result in higher energy demands, evidenced by the strong up-regulation of the oxidative
phosphorylation and electron transport chain. Oxidative stress, pyrimidine metabolism and protein
synthesis and post-translation modification were also highlighted.
Based on the pathway analysis output, we investigated particular transcriptome-fluxome correlations.
Amino acid catabolism profile, one of the most significantly enriched pathways in terms of gene
expression, was analyzed by HPLC and found to be considerable increased, up to 2 fold, in virus producer
cells. Other suggested pathways are currently under study, some of which further substantiate pathways
analysis results, including oxidative stress metabolism and lipid biosynthesis.
In parallel, the integration of transcriptomic and metabolomic data is being used to feed a genomescale
constraint-based reconstruction of the metabolic network, in which a lumped reaction comprising all
building blocks for virus production was included. Such flux-balance analysis based model should help to
elucidate the cell fluxome alterations induced by a virus productive state and the rules to either enforce or
inhibit such state. This work has a direct application in the field of retrovirus manufacture for Vaccinology
and Gene Therapy, providing a framework to guide the rational design of process engineering and cell line
development. It can also be relevant basic virology providing further insights on the cell-virus interaction
and disclosing potential therapeutic targets to inhibit viral replication.