Transcriptomic functional characterization of recombinant adeno-associated virus producing cell line adapted to suspension-growth

Recombinant adeno-associated virus (rAAV) is a widely used delivery vehicle in gene therapy. A scalable production technology is essential for its wide clinical applications. We have taken a synthetic biology approach to generate HEK293-based cell lines which harbor integrated genetic elements encoding essential AAV and adenoviral helper components and can be induced to produce rAAV. Through cycles of cell line enhancement, a high rAAV productivity could be achieved. The cell lines, like their parental HEK293, grew adherently. For scalable production, cell cultivation in suspension is highly desirable. A producer cell line GX6B was adapted to suspension growth in serum-free medium (named GX6Bs). However, it had substantially reduced virus titer. Returning GX6Bs cells to adherent culture conditions using adherent medium and cultured stationarily brought the productivity back to close to the level of adherent GX6B. A survey of the transcriptome revealed that induction and rAAV production elicited a wide range of cellular changes in various functional classes, including host immune defense response and nucleosome organization. The response was more subdued in suspension-growing GX6Bs. Upon reverting to adherent growth, the cellular transcriptome change regained its vigor to be more similar to that seen in GX6B. The GX6Bs maintained in suspension serum-free conditions were then reverted to the adherent culture medium but under an agitated culture environment to keep suspension growth for rAAV production. The productivity returned to within 25%–50% of GX6B. This work demonstrated the feasibility of the suspension culture of synthetic cell lines for the expansion and production of rAAV.