O'Brien, Sofie2020-08-252020-08-252020-05http://hdl.handle.net/11299/215060University of Minnesota Ph.D. dissertation. May 2020. Major: Biomedical Engineering. Advisor: Wei-Shou Hu. 1 computer file (PDF); xv, 121 pages.Protein biologics have transformed the field of medicine in recent years. These complex molecules are produced in living cells, primarily Chinese Hamster Ovary (CHO) cells. Due to the importance of these therapeutic proteins to disease treatment, it is essential to improve the efficiency of their production, both to promote the development of new therapies, and to bring down the cost of manufacturing. One of the most important components of the production process is the development of a cell line. Many features of a cell line, such as cellular growth, metabolism, and the integration site of the gene encoding the protein, influence the resulting culture productivity and quality of the protein produced. In this thesis, multiple aspects of the relationship between integration site and resulting cell line behavior were investigated. First, a rapid integration site identification method was developed to facilitate further analysis of integration sites in complex cell lines. Next, to examine genomic instability, parental cells were compared with high and low producing subclones, leading to identification of genomic regions vulnerable to copy gain/loss. A large-scale analysis across many CHO cell lines was further performed to look for global regions of genomic variation, independent of an individual cell line. To evaluate integration sites with high transcriptional potential, integration sites from high producing cells were examined, and high transgene expression was correlated to high transcriptional activity and accessibility of the integration region. This work also extended to energy metabolism, another key feature of a cell line. Through the use of model guided multi-gene engineering to manipulate cell metabolism, waste product generation was reduced in late-stage culture. With these tools and technologies, we can build a more complete picture of a desirable integration site, which can be used to drive the development of next generation cell lines with high, stable expression of transgenes for therapeutic protein production.enBiotechnologyCell culture engineeringCHO cellsMetabolic engineeringOmicsSystems biologyThesis or Dissertation