EAGER: Enabling Efficient Genome Editing for Advanced Biomanufacturing Applications

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This project addresses the challenge of identifying and correcting problems that affect the efficiency of the cell culture system used to produce the majority of therapeutic proteins. Such biomanufacturing using Chinese hamster ovary (CHO) cells is part of a $100 billion industry. CHO cells are difficult to modify using modern genetic engineering tools and are prone to random changes in their genetic material (DNA). This project will examine proteins that repair damaged DNA as a cause of the difficulties in genetic engineering as well as the genetic instability of CHO cells, and promises to generate new insights into the biology of cell lines as well as developing new tools for these cells. Students will be trained in an interdisciplinary setting that will expose them to multiple potential career paths. This project is anticipated to result in more efficient genome editing in Chinese hamster ovary (CHO) cells; performing synthetic biology on these cells is currently problematic, even using CRISPR and other advanced approaches. The hypothesis will be tested that the DNA double strand break repair system (a component of the molecular machinery that is needed to perform genome editing) is flawed, thereby leading to the failure of synthetic biology approaches in these cells. Defects in the DNA double strand break repair system may also be the cause of the problematic genome instability in CHO cells. The goals of the project are 1) to systematically replace each of the DNA double strand break repair genes from CHO with the corresponding version from the Chinese hamster following a priority list based on sequence similarity and function; and 2) after each replacement, to quantitatively evaluate whether the change has had a measureable impact on efficiency of genome editing and on chromosomal stability.