Adeno-associated Virus (AAV) Capsid Chimeras with Enhanced Infectivity Reveal a Core Element in the AAV Genome Critical for both Cell Transduction and Capsid Assembly

Abstract

Adeno-associated viruses (AAV) have attracted significant attention in the field of gene and cell therapy due to highly effective delivery of therapeutic genes into human cells. The ability to generate recombinant AAV vectors compromised of unique or substituted protein sequences has led to the development of capsid variants with improved therapeutic properties. Seeking novel AAV vectors capable of enhanced transduction for therapeutic applications, we have developed a series of unique capsid variants termed AAV X-Vivo (AAV-XV) derived from chimeras of AAV12 VP1/2 sequences and the VP3 sequence of AAV6. These AAV variants showed enhanced infection of human primary T cells, hematopoietic stem cells, and neuronal cell lines over wildtype parental viruses, and superiority over AAV6 for genomic integration of DNA sequences by AAV alone or in combination with CRISPR gene editing. AAV-XV variants demonstrate transduction efficiency equivalent to AAV6 at multiplicities of infection 2 logs lower, enabling T cell engineering at low AAV doses. The protein coding sequence of these novel AAV chimeras revealed disruptions within the assembly-activating protein (AAP) which likely accounted for observed lower virus yield. A series of genome alterations, reverting the AAP sequence back to wildtype AAV6, had a negative impact on the enhanced transduction seen with AAV-VX, indicating overlapping functions within this sequence for both viral assembly and effective T cell transduction. Our findings show these AAV-XV variants are highly efficient at cell transduction at low dose and demonstrates the importance of the AAP coding region in both viral particle assembly and cell infection. IMPORTANCE A major hurdle to the therapeutic potential of AAV in gene therapy lies in achieving clinically meaningful AAV doses, and secondarily, ability to manufacture commercially viable titers of AAV to support this. By virtue of neutralizing antibodies against AAV that impede patient repeat-dosing, the dose of AAV for in vivo gene delivery has been high, which has resulted in unfortunate recent safety concerns and deaths in patients given higher-dose AAV gene therapy. We have generated new AAV variants possessing unique combinations of capsid proteins for gene and cell therapy applications termed AAV-XV, which have high levels of cell transduction and gene delivery at lower MOI. Furthermore, we demonstrate a novel finding, and an important consideration for recombinant AAV design, that a region of the AAV genome encoding the capsid viral protein and AAP is critical for both virus yield and the enhancement of infection/transduction.

Structural characterization of the porcine adeno‐associated virus Po1 capsid protein binding to the nuclear trafficking protein importin alpha

“…In a recently published article [83], rAAV vectors were generated using protein sequences from chimeric constructs of VP1, VP2 and VP3 sequences from different AAV serotypes. These chimaeras used different N‐terminal domains of Cap proteins containing the common regions of VP1/VP2, of numerous serotypes, AAV2, AAV4, AAV5, AAV6, AAV11 and AAV12.…”

“…In the study by Viney et al . [83], there was an enhanced rate of transduction at low multiplicities of infection for several Cap chimaeras compared with those of wild type, especially for an AAV12/AAV6 chimaera with additional basic residues within BR3 compared with parental AAV6. Viney et al .…”

“…Viney et al . [83] have shown that creating rAAV vectors comprised of different AAV Cap sequences from different serotypes can create more effective gene therapy vectors. The variant chimeric designs with the combination of several VPs from different serotypes were shown to have enhanced transduction characteristics in human cells theorized to be a result of using the N terminus of VP1/VP2 of a different serotype, which also demonstrated an increase in stability of gene delivery.…”

Improved Genome Packaging Efficiency of Adeno-associated Virus Vectors Using Rep Hybrids

“…In the last 2 decades, a lot of research has focused on the characterization and isolation of new cap genes, resulting in hundreds of natural and engineered AAV capsid variants ( 22 , 25 – 28 ). At the same time, the rep gene has been largely ignored due to the fact that the Rep proteins of AAV2 also package recombinant vector genomes into almost all AAV serotypes or variant capsids.…”

Improved Genome Packaging Efficiency of AAV Vectors Using Rep Hybrids

“…In the last two decades a lot of research has focused on the characterization and isolation of new cap genes resulting in hundreds of natural and engineered AAV capsid variants (21,(24)(25)(26)(27). At the same time, the rep gene has been largely ignored due to the fact that the Rep proteins of AAV2 also package recombinant vector genomes into almost all AAV serotypes or variant capsids.…”