BS: Chemical and Biomolecular Engineering, State University of New York at Buffalo
Email username (at udel.edu): wchillia
Office: 559 BPI
The Chinese hamster ovary (CHO) cell lines that are used to produce commercial quantities of therapeutic proteins commonly exhibit a decrease in productivity over time in culture, a phenomenon termed production instability. Random integration of the transgenes encoding the protein of interest into locations in the CHO genome that are vulnerable to genetic and epigenetic instability often causes production instability through copy number loss and silencing of expression. These cell line development challenges can be overcome by using site‐specific integration (SSI) technology to insert the transgenes at genomic loci, often called “hotspots,” that are transcriptionally permissive and have enhanced stability relative to the rest of the genome. However, extensive characterization of the CHO epigenome is needed to identify hotspots that maintain their desirable epigenetic properties in an industrial bioprocess environment and maximize transcription from a single integrated transgene copy. To this end, we have used high-throughput chromosome conformation capture (Hi-C) to characterize the CHO-K1 epigenome and identified large regions of the CHO genome containing transcriptionally permissive three‐dimensional chromatin structures with enhanced genetic and epigenetic stability. These regions significantly reduce the genomic search space when looking for CHO hotspots with widespread applicability and can guide future studies with the goal of maximizing the potential of SSI technology in industrial production CHO cell lines.
More recently, we have been developing high-throughput sequencing technologies to directly measure transgene transcription from thousands of integration sites in a single experiment. By integrating this information with the epigenome data we have collected, we will be able to pinpoint and predict transgene integration sites with maximal production potential that can be retargeted for transgene integration using CRISPR/Cas9 genome editing technology.