Scientific Updates

Nature Biotechnology | CRISPR-free, strand-selective mitochondrial DNA base editing by introducing nickase

  Mitochondria play a pivotal role in regulating cellular energy balance, and changes in mitochondrial DNA can result in serious genetic diseases. According to the MITOMAP database, 95% of confirmed mitochondrial diseases-related mutations are point mutations, which makes the development of base editing tools to correct these mutations extremely significant. However, the current CRISPR system, which is widely used for base editing in nuclear genome, encounters obstacles when it comes to mitochondria. The hydrophobic nature of the mitochondrial inner membrane and its high electrochemical potential hampers the entry of guide RNAs (gRNAs) needed for the CRISPR system. Moreover, known DNA deaminases mostly work on single-stranded DNA, which poses another challenge for developing mitochondrial genome base editors.

  On May 22, 2023, a major breakthrough was reported by the Wensheng Wei laboratory at Peking University. They published a research study in Nature Biotechnology , titled "Strand-selective base editing of human mitochondrial DNA using mitoBEs." This study introduces innovative mitochondrial base editing tools, known as mitoBEs. These tools offer the capability for strand-selective and high precision A-to-G and C-to-T editing in mitochondrial DNA.

  The researchers discovered a way around the obstacles faced by previous editing systems. Most DNA deaminases are only capable of acting on single-stranded DNA, except for DddA. The team hypothesized that if a nick is created on mitochondrial DNA, single-stranded DNA would form. This would then facilitate base editing with these single-stranded DNA deaminases. Through the combination of TALE-fused nickase and deaminase, they successfully developed mitoBEs. They also expanded the applicability of a protein, MutH, by introducing changes in its amino acids, allowing it to be effectively used in mitoBEs. Not only do mitoBEs efficiently achieve A-to-G or C-to-T base editing, but they also have the ability to selectively edit specific strands. Furthermore, this method doesn't lead to large insertions and deletions in mitochondrial DNA, a significant advancement.

  The researchers didn't stop at developing the tool; they also explored its application in treating diseases. They targeted Leber's hereditary optic neuropathy (LHON), an acute eye disease primarily affecting adults, caused by mutations in mitochondrial genes. Using circular RNA-encoded mitoBEs, they successfully achieved efficient and strand-selective mitochondrial DNA base editing and created disease models. Importantly, they managed to correct the MT-ND4 G11778A mutation in cells derived from LHON patients using mitoBEs, thereby significantly restoring mitochondrial function. This indicates that mitoBEs carry potential for therapeutic applications in mitochondrial genetic diseases. Notably, this marks the first instance of successful correction of disease-causing mitochondrial mutations through base editing. In theory, mitoBEs could rectify most mitochondrial disease mutations, presenting a hopeful future for treating these diseases. This technique also holds potential for nuclear base editing, making it a possible tool for treating a broader range of diseases.