Omics-guided engineering of CHO cells reveals host targets to support AAV production

The scalable production of recombinant adeno-associated viruses (rAAVs) remains a critical challenge in gene therapy manufacturing. While HEK293 and insect cell systems dominate current production platforms, each presents significant limitations in cost, scalability, and product quality. Chinese hamster ovary (CHO) cells represent an attractive alternative given their established use in biopharmaceutical manufacturing, yet their inability to efficiently support rAAV assembly has hindered development of CHO-based rAAV bioprocesses. Here, we investigate the molecular basis of this limitation by expressing individual AAV and adenoviral helper proteins in CHO cells and characterizing their effects using integrated transcriptomic and proteomic analyses. Functional enrichment analyses revealed that mitochondrial biogenesis was broadly suppressed across conditions, accompanied by downregulation of antiviral nuclear regulation, signaling networks, including the JAK-STATand interferon-stimulated gene pathways. Functional evaluation of host proteins identified from the omics analyses showed that overexpression of nuclear components like Mx2 and Rad23A supported rAAV production, reaching a yield of 10⁵ vg/mL. Together, these results provide a comprehensive map of CHO cell responses to AAV and adenoviral helper elements, identify candidate host pathways influencing rAAV biogenesis, and highlight both the promise and the remaining barriers toward establishing CHO as a viable platform for large-scale rAAV manufacturing.