The use of microarrays and related genomics tools to reverse engineer mammalian cell culture targeting specific cellular features with application in biotechnology.

摘要

Despite the explosion in genomic studies in recent years, little work has been done to identify and study genes capable of influencing specific cellular properties. In the present work, DNA microarrays were used to identify genes functionally related to distinct phenotypes with the intent of reverse engineering cellular properties in a specific manner.; Two Escherichia coli strains, BL21 and JM109, producing different levels of acetate were compared using oligonucleotide microarrays and the data for six metabolic pathways were analyzed. A semi-parametric algorithm revealed the glyoxylate shunt, TCA cycle, fatty acid, and gluconeogenesis & anaplerotic pathways were expressed differently between the two strains. These findings supported previous observations that BL21 produces much less acetate than JM109 and is therefore able to grow to higher cell densities.; Moving onto mammalian cell culture, anchorage-independent HeLa cells were compared to anchorage-dependent HeLa cells using spotted cDNA microarrays with the goal of modulating adhesion. Cellular adhesion is a feature integral to commercial processes. Assays were developed to quantify the impact of two genes, one encoding a type II membrane glycosylating sialyltransferase ( siat7e) and the other encoding a secreted glycoprotein ( lama4), on adhesion. The expression of siat7e correlated with reduced adhesion whereas expression of lama4 correlated with increased adhesion.; With the same approach two other genes, one encoding a mitochondrial assembly protein (cox15) and the other encoding a kinase (cdk13), were found to influence cellular growth. Enhanced expression of either gene resulted in higher specific growth rates and higher maximum cell densities for HeLa, HEK-293, and CHO cell lines.; Additionally, HEK-293 cells were slowly adapted to serum-free media and sampled at varying serum levels (10%, 5%, 2%, 0%) for analysis using oligonucleotide microarrays. Two genes, egr1 and gas6, with anti-apoptotic properties were identified as potentially improving adaptability by impacting viability at low serum levels without adversely affecting protein production. Collectively, these results indicate that it is possible to modulate distinct cellular features by manipulating the expression of just a few significant genes.