07/07/2026
By Danielle Fretwell

The Francis College of Engineering, Department of Chemical Engineering, invites you to attend a Doctoral Dissertation defense by Yongdan Wang titled: "A Systematic Approach to Improve rAAV Production via Medium Optimization and Cell Line Engineering"

Candidate Name: Yongdan Wang
Degree: Doctoral
Defense Date: Friday, July 17, 2026
Time: 10 a.m. - noon
Location: Please email the advisor or student for location.

Committee:

  • Advisor: Seongkyu Yoon, Professor, Chemical Engineering, University of Massachusetts Lowell
  • Dongming Xie, Associate Professor, Chemical Engineering, University of Massachusetts Lowell
  •  Michael V. Graves, Associate Professor, Biological Science, University of Massachusetts Lowell
  • Pengyuan Liu, Assistant Professor, Chemistry, University of Massachusetts Lowell
  • David McNally, Executive Director, Head of Viral Vector Technology, MassBiologics
  • Luhong He, Executive Director, Upstream Process Development, Eli Lilly

Abstract:
Adeno-associated virus (AAV)–mediated gene therapy has emerged as a leading modality in gene medicine due to its favorable safety profile, broad tissue tropism enabled by diverse serotypes, and ability to achieve long-term therapeutic expression. Despite its clinical success, the widespread adoption of AAV-based therapies is constrained by limited manufacturing capacity and high production costs. The most commonly used manufacturing platform relies on triple-plasmid transient transfection of HEK293 cells, where a vector genome plasmid, Rep/Cap plasmid, and helper plasmid are co-delivered to produce recombinant AAV (rAAV) without genomic integration. However, the efficiency of this system remains suboptimal, largely due to host cell–dependent bottlenecks that limit viral vector yield.

This dissertation investigates the cellular and molecular constraints underlying rAAV production in HEK293 cells and develops strategies to improve manufacturing productivity. Chapter 1 provides a comprehensive exploration of the intricate cellular process involved in rAAV production from the host cell perspectives. The knowledge in the fundamental biology of host cells supporting viral replication as manufacturing factories or exhibiting defending behaviors against viral production was summarized for each major vector production stage. The control strategies from the host cell perspective are proposed as insights based on characterized molecular features and existing knowledge of AAV viral life cycle, rAAV and other viral vector production in the Human embryonic kidney (HEK) cells.

Chapter 2 establishes a transcriptomic analysis workflow to systematically characterize host cell responses during rAAV production. This mechanism-driven approach identifies significantly regulated pathways and cellular features associated with productive viral vector synthesis, providing a foundational dataset for subsequent optimization strategies.

Chapter 3 leverages these transcriptomic insights to screen medium supplements targeting top-ranked antiviral and immune-response pathways using high-throughput deep-well plate systems. The observed improvements in rAAV yield validate the predictive power of transcriptomic analysis and confirm that host antiviral responses represent key limitations in current production systems.

Chapter 4 extends this work through CRISPR-Cas9–mediated knockout screening of prioritized antiviral related genes identified in earlier transcriptomic analyses. Bulk edited cell populations are evaluated for their ability to enhance rAAV production, both quantitatively and qualitatively, thereby demonstrating the potential of host genome engineering to improve viral vector manufacturing performance.

Collectively, this work integrates systems-level transcriptomic profiling, process optimization, and genome engineering to elucidate and overcome host cell–derived barriers in rAAV production, offering a comprehensive framework for improving the scalability and efficiency of gene therapy vector manufacturing.