Genome-wide CRISPR screenings identified SMCHD1 as a host-restricting factor for AAV transduction.

AAV-mediated gene therapy typically requires a high dose of viral transduction, risking acute immune responses and patient safety, part of which is due to limited understanding of the host-viral interactions, especially post-transduction viral genome processing. Here, through a genome-wide CRISPR screen, we identified SMCHD1 (Structural Maintenance of Chromosomes Hinge Domain 1), an epigenetic modifier, as a critical broad-spectrum restricting host factor for post-entry AAV transgene expression. SMCHD1 knock-down by RNAi and CRISPRi or knock-out by CRISPR all resulted in significantly enhanced transgene expression across multiple viral serotypes, as well as for both single-strand and self-complementary AAV genome types. Mechanistically, upon viral transduction, SMCHD1 effectively repressed AAV transcription by the formation of an LRIF1-HP1-containing protein complex and directly binding with the AAV genome to maintain a heterochromatin-like state. SMCHD1-KO or LRIF1-KD could disrupt such a complex and thus result in AAV transcriptional activation. Together, our results highlight the host factor-induced chromatin remodeling as a critical inhibitory mechanism for AAV transduction and may shed light on further improvement in AAV-based gene therapy. Author summary: Adeno-associated virus (AAV) is one of the most commonly used carrier for gene therapy. However, current approved therapies typically use extremely high doses in order to achieve sufficient beneficial efficiency. This is partially due to a lack of understanding about host reponsese that restrict AAV-mediated gene delivery and expression. In this study, we carried out genome-wide CRISPR screens to identify potential host restricting factors for AAV transduction in human cells and identified SMCHD1 as one of the key epigenetic modifers that formed a complex with LRIF1, bound with HP1-associated AAV genome to form a heterochromatin-like states, and suppressed its transcription. Disruption of the SMCHD1-LRIF1 complex would increase the genome accessibility of AAVs and viral transduction, and significantly increase AAV-mediated transgene expression. Therefore, our results indicated that the host factor-induced chromatin remodeling might be a critical inhibitory mechanism for AAV transduction and may help to further improve AAV-based gene therapy. [ABSTRACT FROM AUTHOR]