碱基编辑-正序生物

碱基编辑

碱基编辑

碱基编辑技术通过“效应器”和“定位器”相结合，在靶向位点完成碱基转换，从而实现基因组编辑和改写。

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碱基编辑与CRISPR介导的基因编辑相比的优势

目前已知超过75,000种基因突变会导致人类疾病，如地中海贫血、杜兴氏肌肉营养不良症等。绝大部分由基因突变所导致的遗传性疾病无药可医，而对于其中小部分病种，患者往往需要终生服药，并承受药物带来的副作用和心理压力。遗传性疾病中约一半是由单碱基突变导致，这类突变难以利用传统的基因编辑工具进行修复。而碱基编辑技术不仅能够在庞大的基因组中精准、永久地改变单个碱基对，还可以根据不同疾病的突变位点对其进行自由组合，为点突变引起的遗传性疾病的治愈以及癌症的免疫治疗提供了新的可能。

前几代基因编辑技术分别为ZFNs、TALENs和CRISPR/Cas9，其共同特点是通过完全切断DNA双链造成double strand break来进行重新整合修复基因，被称为“分子剪刀”或“分子魔剪”。这些技术均可能造成由DNA双链断裂而带来的大片段染色体缺失、染色体易位等安全问题。

如果说CRISPR/Cas9是一把剪刀，需要通过把DNA双链剪断才能进行编辑，那Base Editing碱基编辑技术就是一支笔，在完全保证DNA双链完整性的同时就可以对错误的碱基进行校正，因此不会促发p53通路激活和染色体异常等安全风险，实现了“化刀为笔”的精确修复，同时也确保了高效编辑和安全性。碱基编辑技术从根本上解决了前几代基因编辑技术引发DNA双链断裂而造成的大片段染色体缺失、染色体易位等源头问题，在人类疾病治疗的应用上，其安全性和成药性都有本质的提升。有一个更加具象的比喻，碱基编辑把基因编辑从风险性高的开胸手术变成了简易安全的微创手术，精准修复，降低风险。

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知识产权

拥有碱基编辑体系底层平台性自主知识产权的碱基编辑器

正序生物科学创始人团队至今已开发出5大系列的碱基编辑系统，其中增强型碱基编辑器eBE（enhanced Base Editor）于2020年12月获得中国专利授权，变形式碱基编辑器tBE（transformer Base Editor）于2022年7月获得美国专利授权，其他多项碱基编辑技术也提交了PCT国际专利申请，覆盖全球15个国家和地区。

新型高精准变形式碱基编辑系统

其中，由正序生物科学创始人团队开发的新型高精准碱基编辑器tBE（transformer Base Editor），将普通碱基编辑器存在的全基因组以及全转录组的脱靶突变完全消除，同时还保持了在靶向位点处的高编辑效率(tBE, Nature Cell Biology, 2021)，成为目前已开发的胞嘧啶碱基编辑器中消除脱靶突变和实现靶向编辑综合能力最好的碱基编辑器。通过巧妙的“锁”的设计，tBE只在靶向位点时编辑功能才能“解锁”，而在非靶向位点时编辑功能失效，从而实现了高效无脱靶的精准编辑效果。同时，tBE灵活的“变形金刚式”多元件组合方法更完美地契合包括AAV、mRNA/LNP等多种体内递送方式的需求，大大提高了其体内碱基编辑的效率。此外，tBE在可成药靶点处还可以同时实现多个靶点的精准高效编辑。相对于现有的碱基编辑系统，这些优势都极大地扩展了tBE在临床治疗的应用范围。

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▲ 正序生物新型高精准变形式碱基编辑器tBE（transformer Base Editor）

（Han et al., Nature Protocols, 2023）

研究成果

研究论文

综述、评论、访谈

1. Guangye Li#, Guo Chen#, Guo-Hua Yuan#, Jia Wei#, Qingyang Ni, Jing Wu, Bei Yang, Li Yang*, Jia Chen*. Specific and efficient RNA A-to-I editing through cleavage of an ADAR inhibitor. Nat Biotechnol, 2025, doi: 10.1038/s41587-025-02591-2.

2. Yuhang Fan#, Wenchao Xu#, Bao-Qing Gao#, Huichao Qin, Xiaoyi Wu, Jia Wei, Qingyang Ni, Lina Zhou, Jiangchao Xiang, Jing Wu, Bei Yang, Li Yang, Jia Chen*. Leveraging base excision repair for efficient adenine base editing of mitochondrial DNA. Nat Biotechnol, 2025, doi: 10.1038/s41587-025-02608-w.

3. Qimingxing Chen#, Yan Chang#, Xiaoyan He, Yan Ding, Runyuan Wang, Ran Luo, Jialu Yuan, Jiabei Chen, Guisheng Zhong, Huiying Yang, Jia Chen*, Jianfeng Li*. Targeted Delivery of mRNA with Polymer–Lipid Nanoparticles for In Vivo Base Editing. ACS NANO. Feb 2025. 19(8): 7835–7850.

4. Chengfang Liu#, Sifan Cheng#, Junjie Zhu, Lina Zhou, Jia Chen*. A quick guide to evaluating prime editing efficiency in mammalian cells. Methods in Enzymology, 2025, doi.org/10.1016/bs.mie.2025.01.016

5. Jiangchao Xiang#, Wenchao Xu#, Jing Wu#, Yaxin Luo, Bei Yang*, Jia Chen*. Nucleoside deaminases: the key players in base editing toolkit. Biophys Rep, 2023, 9(6):325-337.

6. Wenyan Han#, Hou-Yuan Qiu#, Shangwu Sun#, Zhi-Can Fu#, Guo-Quan Wang#, Xiaowen Qian#, Lijie Wang, Xiaowen Zhai, Jia Wei, Yichuan Wang, Yi-Lin Guo, Guo-Hua Cao, Rui-Jin Ji, Yi-Zhou Zhang, Hongxia Ma, Hongsheng Wang, Mingli Zhao, Jing Wu, Lili Bi, Qiu-Bing Chen, Zifeng Li, Ling Yu, Xiaodun Mou, Hao Yin, Li Yang*, Jia Chen*, Bei Yang*, Ying Zhang*. Therapeutic base editing of the HBG promoter reactivates γ-globin expression with no detectable off-target mutations in beta-thalassemia HSCs. Cell Stem Cell, 2023, 30(12):1624-1639.e8.

7. Wenyan Han#, Baoqing Gao#, Junjie Zhu#, Zongxing He#, Jianfeng Li*, Li Yang*, Jia Chen*. Design and application of the transformer base editor in mammalian cells and mice. Nat Protoc, 2023, 18(11):3194-3228.

8. Wenwen Zhao#, Jifang Li#, Xiao Wang#, Wei Xu#, Baoqing Gao#, Jiangchao Xiang, Yaofeng Hou, Wei Liu, Jing Wu, Qilian Qi, Jia Wei, Xiaoyu Yang, Lu Lu*, Li Yang*, Jia Chen*, Bei Yang*. Prime editor-mediated functional reshaping of ACE2 prevents the entry of multiple human coronaviruses, including SARS-CoV-2variants. MedComm, 2023, 4:e356.

9. Li X#*, Zhou L#, Gao BQ#, Li G, Wang X, Wang Y, Wei J, Han W, Wang Z, Li J, Gao R, Zhu J, Xu W, Wu J, Yang B, Sun X*, Yang L*, Chen J*. 2022. Highly efficient prime editing by introducing same-sense mutations in pegRNA or stabilizing its structure. Nat Commun, 13(1):1669.

10. Gao R#, Fu ZC#, Li X#, Wang Y#, Wei J, Li G, Wang L, Wu J, Huang X*, Yang L*, Chen J*. 2022. Genomic and Transcriptomic Analyses of Prime Editing Guide RNA-Independent Off-Target Effects by Prime Editors. CRISPR J, 5(2):276-293.

11. Wang J#, He Z#, Wang G#, Zhang R#, Duan J, Gao P, Lei X, Qiu H, Zhang C, Zhang Y, Yin H*. 2022. Efficient targeted insertion of large DNA fragments without DNA donors. Nat Methods, 19(3): 331-340.

12. Gao X#, Ma XK#, Li X, Li GW, Liu CX, Zhang J, Wang Y, Wei J, Chen J, Chen LL and Yang L*. 2022. Knockout of circRNAs by base editing back-splice sites of circularized exons. Genome Biol, 23: 16.

13. Wang L#, Xue W#, Zhang H#, Gao R#, Qiu H#, Wei J, Zhou L, Lei YN, Wu X, Li X, Liu C, Wu J, Chen Q, Ma H, Huang X, Cai C, Zhang Y, Yang B*, Yin H*, Yang L* and Chen J*. 2021. Eliminating base-editor-induced genome-wide and transcriptome-wide off-target mutations. Nat Cell Biol, 23(5): 552-563.

14. Wang X#, Ding C#, Yu W#, Wang Y#, He S#, Yang B#, Xiong YC, Wei J, Li J, Liang J, Lu Z, Zhu W, Wu J, Zhou Z, Huang X, Liu Z*, Yang L* and Chen J*. 2020. Cas12a Base Editors Induce Efficient and Specific Editing with Low DNA Damage Response. Cell Rep, 31(9): 107723.

15. Song CQ#, Jiang T#, Richter M, Rhym LH, Koblan LW, Zafra MP, Schatoff EM, Doman JL, Cao Y, Dow LE, Zhu LJ, Anderson DG, Liu DR*, Yin H*, and Xue W*. 2020. Adenine base editing in an adult mouse model of tyrosinaemia. Nat Biomed Eng, 4: 125-130.

16. Wang Y#, Gao R#, Wu J#, Xiong YC, Wei J, Zhang S, Yang B, Chen J* and Yang Y*. 2019. Comparison of cytosine base editors and development of the BEable-GPS database for targeting pathogenic SNVs. Genome Biol, 20(1): 218.

17. Wang X#, Li J#, Wang Y#, Yang B#, Wei J#, Wu J, Wang R, Huang X*, Chen J* and Yang L*. 2018. Efficient base editing in methylated regions with a human APOBEC3A-Cas9 fusion. Nat Biotechnol, 36(10): 946-949.

18. Li X#, Wang Y#, Liu Y#, Yang B#, Wang X, Wei J, Lu Z, Zhang Y, Wu J, Huang X*, Yang L* and Chen J*. 2018. Base editing with a Cpf1-cytidine deaminase fusion. Nat Biotechnol, 36(4): 324-327.

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20. Lei L#, Chen H#, Xue W#, Yang B#, Hu B#, Wei J, Wang L, Cui Y, Li W, Wang J, Yan L, Shang W, Gao J, Sha J, Zhuang M, Huang X, Shen B*, Yang L* and Chen J*. 2018. APOBEC3 induces mutations during repair of CRISPR-Cas9-generated DNA breaks. Nat Struct Mol Biol, 25(1): 45-52.

21. Yin H#, Song CQ#, Suresh S, Kwan SY, Wu Q, Walsh S, Ding J, Bogorad RL, Zhu LJ, Wolfe SA, Koteliansky V, Xue W*, Langer R* and Anderson DG*. 2018. Partial DNA-guided Cas9 enables genome editing with reduced off-target activity. Nat Chem Biol, 14(3):311-316.

22. Wang L#, Xue W#, Yan L#, Li X, Wei J, Chen M, Wu J, Yang B*, Yang L* and Chen J*. 2017. Enhanced base editing by co-expression of free uracil DNA glycosylase inhibitor. Cell Res, 27(10): 1289-1292.

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24. Yin H, Song CQ, Dorkin JR, Zhu L, Li Y, Wu Q, Park A, Yang J, Suresh S, Bizhanova A, Gupta A, Bolukbasi M, Walsh S, Bogorad R, Gao G, Weng Z, Dong Y, Koteliansky V, Wolfe S, Langer R, Xue W* and Anderson DG*. 2016. Therapeutic genome editing by combined viral and non-viral delivery of CRISPR system components in vivo. Nat Biotechnol, 34(3):328-33.

25. Zhang XO#, Wang HB#, Zhang Y, Lu X, Chen LL* and Yang L*. 2014. Complementary sequence-mediated exon circularization. Cell, 159(1): 134-147.

26. Yin H#, Xue W#, Chen S, Bogorad RL, Benedetti E, Grompe M, Koteliansky V, Sharp PA, Jacks T and Anderson DG*. 2014. Genome editing with Cas9 in adult mice corrects a disease mutation and phenotype. Nat Biotechnol, 32(6): 551-553.

27. Xue W#, Chen S#, Yin H#, Tammela T, Papagiannakopoulos T, Joshi NS, Cai W, Yang G, Bronson R, Crowley DG, Zhang F, Anderson DG, Sharp PA and Jacks T*. 2014. CRISPR-mediated direct mutation of cancer genes in the mouse liver. Nature, 514(7522): 380-384.

28. Chen J, Miller BF and Furano AV*. 2014. Repair of naturally occurring mismatches can induce mutations in flanking DNA. Elife, 3: e02001.

1. Jin-Soo Kim*, Jia Chen*. Base editing of organellar DNA with programmable deaminases. Nat Rev Mol Cell Biol, 2024, 25(1):34-45.

2. Li Yang*, Jia Chen*. Expanding genome editing scopes with artificial intelligence. Sci Bull, 2023, 68(23):2881-2883.

3. Gao C* and Chen J*. 2021. CRISPR Adventures in China. CRISPR J, 4(3): 304-306.

4. Chen Q, Zhang Y* and Yin H*. 2021. Recent advances in chemical modifications of guide RNA, mRNA and donor template for CRISPR-mediated genome editing. Adv Drug Deliv Rev, 168: 246–258.

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6. Yang L*, Yang B* and Chen J*. 2019. One Prime for All Editing. Cell, 179(7): 1448-1450.

7. Chen J*, Yang B* and Yang L*. 2019. To BE or not to BE, that is the question. Nature Biotechnology, 37(5): 520-522.

8. Yang B*, Yang L* and Chen J*. 2019. Development and Application of Base Editors. CRISPR J, 2(2): 91-104.

9. Zhang HX, Zhang Y* and Yin H*. 2019. Genome Editing with mRNA Encoding ZFN, TALEN, and Cas9. Mol Ther, 27(4): 735–746.

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12. Yang B*, Li X, Lei L and Chen J*. 2017. APOBEC: From mutator to editor. J Genet Genomics, 44(9): 423-437.

13. Yin H, Kauffman KJ and Anderson DG*. 2017. Delivery technologies for genome editing. Nat Rev Drug Discov, 16(6): 387-399.

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(#: co-first author, *: corresponding author)

技术开发

技术开发

碱基编辑

知识产权

编辑疗法

研究成果