Cell Stem Cell | A novel strategy for treating β-hemoglobinopathy based on the transformer base editor (tBE)

2023-11-24 10:05:44 Correctseq 577

CorrectSequence Therapeutics (Correctseq), a biotechnology company using innovative base editing technology to help people with severe disease, today announced that the company and the research teams from ShanghaiTech University, Wuhan University, Fudan University and Children's Hospital of Fudan University published an article entitled “Base editing of the HBG promoter induces potent fetal hemoglobin expression with no detectable off-target mutations in human HSCs” in Cell Stem Cell on November 20th, 2023, reporting a novel base editing strategy for treating β-hemoglobinopathies with transformer base editor (tBE). Compared with Cas nuclease-mediated gene editing therapy, tBE editing exhibited higher γ-globin induction, lower cytotoxicity and undetected off-target mutations. Up to now, the pipeline for β-hemoglobinopathies developed by Correctseq based on tBE has exhibited long-term safety and efficacy in mice for more than 6 months and will enter clinical trials by the end of the year. With in-depth understanding in the therapeutic mechanisms of β-hemoglobinopathies using various genome editors at multiple targets, the pipeline under development in Correctseq with tBE has demonstrated great potential as the best-in-class gene editing therapy for the patients around the world.

β-hemoglobinopathies, including β-thalassemia and sickle cell disease (SCD), are the severe human autosomal monogenic genetic diseases caused by the mutations in hemoglobin subunit beta (HBB) gene locus. More than 3% of the global population carries the beta-hemoglobinopathy-associated alleles, and hundreds of thousands of newborns are diagnosed each year.

Reactivating silenced γ-globin expression offers a universal therapeutic strategy for treating β-hemoglobinopathies. γ-Globin expression is tightly regulated during development and is silenced shortly after birth by the repressors that bind to HBG1/2 promoter regions. BCL11A and ZBTB7A are the two major repressors of γ-globin gene expression, responsible for its silencing.

A therapeutic strategy disrupts the erythroid-specific BCL11A enhancer located on chromosome 2 via CRISPR/Cas9 greatly reduces BCL11A expression in erythroid cells without affecting other lineage development. Using Cas9 nuclease to disturb repressor binding motifs in hematopoietic stem and progenitor cells (HSPCs) relies on generating DSBs, thereby raising the risk of p53-dependent DNA damage response and cell toxicity in HSPCs. Moreover, the studies about β-thalassemia patients with naturally reactivated γ-globin expression have indicated that the fetal hemoglobin (HbF, α2γ2) level correlates negatively with the number of morbidities. Therefore, it is important to develop a safe and efficacious therapeutic strategy for β-hemoglobinopathies, which efficiently promotes HbF expression at a level sufficient for cure, meanwhile circumventing safety issues such as DSBs and off-target mutations.

At first, the researchers designed pairs of sgRNAs and helper sgRNAs targeting six major regulatory motifs in the regulatory network of HBG1/2 (Figure 1, top box). After examining on-target and gRNA-dependent off-target editing with five other previously published CBEs, the authors found tBE displayed no detectable off-target mutations across all six sgRNAs, as well as high on-target editing efficiency. Then, the researchers optimized the RNA expression system of tBE and electroporation conditions, which greatly improved the editing efficiency of tBE in HSPCs. To evaluate the therapeutic potential of tBE-based editing strategies, they electroporated mRNA encoding tBE and chemically modified sgRNA/hsgRNA pairs into the HUDEP-2 cell line, and measured the reactivated γ-globin mRNA expression. the authors found that editing the BCL11A binding motif located at the HBG1/2 promoter produced the highest γ-globin mRNA levels, which was chosen as the therapeutic target for tBE-editing strategy. The authors further compared tBE-editing strategy with other preclinical and clinical method, including the therapeutic sgRNA targeting BCL11A erythroid enhancer that has been approved to treat sickle cell disease—sgBCL11A-1617 (Figure 1, bottom left box). The tBE-edited HSPCs were then in vitro differentiated into erythroid cells to measure the γ-globin mRNA and protein expression levels, and the authors found that tBE-editing strategy produced significantly more γ-globin mRNA and protein than other gene editing strategies.


Figure 1. Schematic diagram of the main steps of this study.


To determine whether tBE-edited HSPCs retained repopulation ability and whether the editing persisted over the differentiation process, the researchers xenotransplanted tBE-edited HSPCs into immunodeficient mice (Figure 1, bottom left box). No significant differences were observed between the edited and the mock-treated HSPCs in terms of engraftment and differentiation potential after 4 months, which suggests that the edited alleles were maintained in hematopoietic stem cells (HSCs) and in their progenies.

Furthermore, the authors compared the efficacies of different gene editing strategies to treat CD34+ HSPCs from β-thalassemia patient and found that the editing of the BCL11A binding site at HBG1/2 promoter by tBE_sgHBG-1 exhibited the highest γ-globin reactivation. At the same time, the research team conducted a comprehensive assessment of the level of DNA damage and DNA/RNA off-target events during tBE editing of HSPCs. The experimental results showed that tBE-edited HSPCs only transiently and slightly up-regulated the expression level of p21, and no DNA/RNA off-target mutations higher than the background level were detected (Figure 1, bottom right).

Collectively, tBE-mediated editing at the BCL11A binding site in the HBG1/2 promoter triggers robust induction of HbF with no detectable off-target mutation, demonstrating the potential to become the “Best in Class” approach for the treatment of β-hemoglobinopathy in clinics.


Paper link: https://www.cell.com/cell-stem-cell/fulltext/S1934-5909(23)00369-7


About CorrectSequence Therapeutics

CorrectSequence Therapeutics (Correctseq) aims to use our innovative base editing technology to help people with severe diseases.

We have developed multiple base editing systems and our base editors offer significant advantages in controlling off-target effects and improving in vivo editing efficiency. Our base editing studies were published in high-profile scientific journals including Nature Biotechnology, Nature Cell Biology, Nature Structural & Molecular Biology, Cell Research and Cell Reports.

Our goal is to discover, develop, manufacture, and commercialize curative genetic medicines for various diseases. Multiple pipelines for genetic diseases, cancer immunotherapy, metabolic diseases, and infectious diseases are well underway. We have set up R&D and manufacturing centers in Shanghai, as well as the regulatory and clinical center in China Central Place, Beijing. Our world-class R&D laboratory, CMC process development laboratory and cGMP manufacturing facility guarantee the rapid translation and application of our innovative research.

We focus on biotechnology innovation, research and development and are committed to providing efficient, reliable and safe solution for unmet medical needs.

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