Adaptive Machine Learning Framework for Optimizing the Affinity Purification of Adeno-Associated Viral Vectors

Abstract

Adeno-associated viral (AAV) vectors for gene therapy are becoming integral to modern medicine, providing therapeutic options for diseases once deemed incurable. Currently, viral vector purification is a critical bottleneck in the gene therapy industry, impacting product efficacy and safety as well as accessibility and cost to patients. Traditional methods for improving viral vector purity are resource-intensive and often fail to adjust the purification process parameters to maximize the resulting product yield and quality. To address this challenge, we developed a machine learning framework that leverages Bayesian optimization to systematically refine affinity chromatography parameters (sample load, flow rate, and the formulation of chromatographic media) to improve AAV purification. The efficiency of this closed-loop workflow in iteratively optimizing the vector's yield, purity, and transduction efficiency was demonstrated by purifying clinically relevant serotypes AAV2, AAV5, AAV6, and AAV9 from HEK293 cell lysates using the affinity adsorbent AvXcel. We show that in three (or fewer) cycles of Bayesian optimization, we elevated yields from a baseline of 70% to a remarkable 97%-99%, while reducing host cell impurities by 230- to 400-fold across all serotypes. Performing the purification process with optimized parameters consistently produced vectors with high purity and preserved high transduction activity, essential for therapeutic efficacy and safety, demonstrating the applicability of the framework across multiple serotypes-a key challenge in AAV manufacturing. This study represents the first reported application of closed-loop, data-driven Bayesian optimization for enhancing AAV productivity and quality at the affinity capture step, with demonstrated transferability of historical purification data and process knowledge. The proposed adaptive machine learning framework is efficient and applicable across serotypes, enabling rapid process development, reduced costs, and advancing the accessibility and clinical translation of AAV-based gene therapies.

Keywords: Bayesian optimization; Gaussian process; bioseparations; closed‐loop process development; gene therapy.