Development of STAR Editors (CRISPR-Cas9/lgRNA-ssDNA) for the cure of chronic hepatitis B

Abstract This phase 1 SBIR project is to investigate the feasibility of an innovative CRISPR-Cas9 scar-less editing technology to permanently inactivate both hepatitis B virus (HBV) covalently closed circular DNA (cccDNA) and integrated DNA for the cure of chronic hepatitis B (CHB). Although the currently available antiviral agents, including nucleos(t)ide analogue viral DNA polymerase inhibitors and pegylated alpha-interferon, can efficiently inhibit HBV replication and prevent disease progression in the majority of treated patients, the cure of chronic HBV infection is rarely achieved and life-long antiviral therapy is thus required. The failure of a cure is due to the current antiviral regimens cannot eliminate cccDNA from the nuclei of infected hepatocytes. cccDNA, the transcription template of viral RNA, is the most stable HBV replication intermediate and the resource of viral replication rebound after disruption of antiviral therapies. Moreover, despite not being essential for viral replication, the transcripts from integrated HBV DNA in cellular chromosomes have recently been proven to support the secretion of majority of HBV surface antigen (HBsAg) in HBeAg-negative CHB patients. Prolonged excessive expression of HBsAg induces the exhaustion of viral antigen-specific T and B cells and favors the persistent infection of HBV. Apparently, elimination or permanent inactivation of cccDNA as well as integrated HBV DNA is essential to achieve the cure of CHB. CRISPR-Cas9 gene editing technology is thus far the most promising approach to achieve this therapeutic goal. However, although the classic CRISPR-Cas9 gene editing technologies had been proven to cleave and edit cccDNA in cultured cells and animal models, their cleavage of integrated HBV DNA may lead to chromosome break and unintended mutations, causing genetic instability and genotoxicity. Recently, CRISPR-Cas9 base editor technology had been developed to overcome this limitation. Unfortunately, the low editing efficiency, high rate of guide- independent editing and usage of lentiviral vector for delivery hampered its further development. In this project, we propose to develop our proprietary ligated-guide RNA (lgRNA)-based STAR (Seek-Tag-Amend- Release) editor technology for efficient and accurate inactivation of both forms of nuclear HBV DNA by introducing stop codons into overlapping HBsAg and viral DNA polymerase genes. Specifically, we will first verify the cleavage activity and specificity of STAR editors in vitro to optimize the structures of lgRNA as well as the conjugation sites of single strand DNA (ssDNA) (the template of editing) (Aim 1). We will then evaluate the editing efficiency and specificity of STAR editors in human hepatoma cell line harboring both integrated HBV DNA and cccDNA (Aim 2). Successful completion of this Phase 1 project will enable us to apply for a Phase 2 study to evaluate selected multiplexing STAR editors for their inactivation activity of integrated HBV DNA in HBV transgenic mice and cccDNA in HBV infected humanized uPA-SCID mice in vivo.