Efficient development of nanobody-based affinity chromatography for AAV8 purification

Adeno-associated virus serotype 8 (AAV8) is a highly effective vector for gene therapy. However, its purification remains challenging due to its low natural abundance and stringent purity requirements. This study aimed to develop an affinity chromatography resin utilizing nanobodies (Nbs) to enhance AAV8 purification efficiency. An AAV8-specific Nb library was constructed, leading to the identification of Nb9 as the most promising candidate based on its high binding affinity, stability and yield. Nb9 was expressed in Pichia pastoris, resulting in high yield and exceptional purity. Two types of agarose resins, Epoxy activated Bestarose 6B and PabPur SulfoLink Beads 4FF, were employed for Nb9 conjugation. Epoxy activated Bestarose 6B resin exhibited a significantly higher ligand density (9.12 mg/mL). Binding capacity assessments of the LQ01 resin demonstrated optimal performance at pH 7.0, with diminishing efficacy at lower and higher pH levels. Different NaCl concentrations influenced the binding efficiency, providing critical insights for refining purification conditions. Purification trials exhibited high specificity, purity and consistent VP protein ratio, as evidenced by SDS-PAGE analysis, confirming effective AAV8 capture and elution. Furthermore, the resin demonstrated robust performance across repeated cycles, retaining 71.9 % of its initial binding capacity after 20 uses and maintaining stability with only a 6 % reduction after 7 days at 37 °C. These findings highlight LQ01's potential for scalable and cost-effective AAV8 purification, while demonstrating the broader applicability of Nbs in affinity chromatography and biotechnological processes. •Constructed a diverse nanobody library targeting AAV8 with high specificity.•Optimized Nb9 expression in Pichia pastoris, reaching 7 g/L yield.•LQ01 resin showed excellent binding and elution capacity for AAV8 purification.•Establishes a robust framework for developing specific affinity resins.