Epigenetic Silencing of Recombinant Adeno-associated Virus Genomes by NP220 and the HUSH Complex

• Published in: Journal of virology Vol. 96; no. 4; p. e0203921
• Main Authors: Das, Anshuman, Vijayan, Madhuvanthi, Walton, Eric M., Stafford, V. Grace, Fiflis, David N., Asokan, Aravind
• Format: Journal Article
• Language: English
• Published: United States American Society for Microbiology 23.02.2022
• Subjects: Antigens, Neoplasm - genetics; Antigens, Neoplasm - metabolism; Capsid - metabolism; Dependovirus - genetics; Dependovirus - metabolism; DNA-Binding Proteins - genetics; DNA-Binding Proteins - metabolism; Epigenesis, Genetic; Gene Silencing; Genome, Viral - genetics; HEK293 Cells; Humans; Multiprotein Complexes - genetics; Multiprotein Complexes - metabolism; Nuclear Proteins - genetics; Nuclear Proteins - metabolism; Phosphoproteins - genetics; Phosphoproteins - metabolism; RNA-Binding Proteins - genetics; RNA-Binding Proteins - metabolism; Serogroup; Transcription Factors - genetics; Transcription Factors - metabolism; Transcription, Genetic; Transgenes - genetics; Virology; Virus-Cell Interactions; gene silencing; gene therapy; virus-host interactions; AAV; DNA damage
• ISSN: 0022-538X; 1098-5514; 1098-5514
• DOI: 10.1128/jvi.02039-21

Recombinant AAV vectors can enable long-term gene expression in a wide variety of tissues. However, transgene silencing has been reported in some human gene therapy clinical trials. Here, we demonstrate the HUSH complex can suppress transcript formation from rAAV vector genomes by epigenetic modification of associated host histones. Further, the AAV capsid appears to play an important role in this pathway. We postulate that modulation of epigenetic pathways could help improve rAAV expression. The single-stranded DNA genome of adeno-associated viruses (AAV) undergoes second-strand synthesis and transcription in the host cell nucleus. While wild-type AAV genomes are naturally silenced upon integration into the host genome, recombinant AAV (rAAV) genomes typically provide robust expression of transgenes persisting as extrachromosomal DNA or episomes. Episomal DNA associating with host histones is subject to epigenetic modifications, although the mechanisms underlying such are not well understood. Here, we provide evidence that the double-stranded DNA binding protein NP220, in association with the human silencing hub (HUSH) complex, mediates transcriptional silencing of single-stranded as well as self-complementary rAAV genomes. In cells lacking NP220 or other components of the HUSH complex, AAV genome transcript levels are increased and correlate with a marked reduction in repressive H3K9 histone methylation marks. We also provide evidence that the AAV capsid (serotype) can profoundly influence NP220-mediated silencing of packaged genomes, indicating potential role(s) for capsid-genome or capsid-host factor interactions in regulating epigenetic silencing of rAAV genomes. IMPORTANCE Recombinant AAV vectors can enable long-term gene expression in a wide variety of tissues. However, transgene silencing has been reported in some human gene therapy clinical trials. Here, we demonstrate the HUSH complex can suppress transcript formation from rAAV vector genomes by epigenetic modification of associated host histones. Further, the AAV capsid appears to play an important role in this pathway. We postulate that modulation of epigenetic pathways could help improve rAAV expression.