左二伟课题组

Zuo Erwei Lab

左二伟，中国农业科学院深圳农业基因组研究所研究员、博士生导师。近年来，致力于利用分子生物学、计算生物学等手段开展新型基因编辑技术的研发与应用研究，推动基因编辑技术医学应用安全性评价体系建设。提出脱靶效应产生的分子基础，研发多种检测技术，证实了单碱基编辑器会导致基因组范围内完全随机无法预测的脱靶效应；发现了脱氨酶产生脱靶效应的直接证据，理清了脱氨酶的核酸结合结构域与脱靶效应之间的关系，研发了效率、精度具佳的单碱基编辑工具，在一定程度上解决了医学应用重大问题；实现了对多种人类疾病小鼠模型的治疗研究，取得了良好效果，为开展临床实验提供依据，有望治疗相关疾病。构建了C-CRISPR技术，显著提高了基因编辑效率，研制了F0代基因完全敲除灵长类动物，为快速建立灵长类动物疾病模型做出贡献。其中单碱基基因编辑造成大量脱靶效应及其优化解决方法入选“2019中国生命科学十大进展”。合理设计胞嘧啶碱基编辑器可在保持高靶向活性同时降低DNA和RNA的非靶向效应入选中国农业科学院“2020重大科学发现”，获得2021基因组研究所“重大成果奖”。一步法生产基因完全敲除动物研究成果在2017年国际干细胞研究学会年会（2017 ISSCR）获得“Merit Award”。近年来，基因编辑领域在Science、Nature等期刊发表多篇研究论文。

Erwei Zuo is a researcher of Institute of Agricultural Genome Research, Chinese Academy of Agricultural Sciences. As a molecular biologist, Zuo focused on the development of genome editing tools, and the construction of a safety evaluation system for gene-editing applications. He and his team have proposed the molecular basis of the off-target effect, developed various detection technologies, and confirmed that single-base editors can cause completely random and unpredictable off-target effects within the genome. He revealed direct evidence of off-target effects of the deaminase, and clarified the relationship between the nucleic acid-binding domain of deaminase and off-target effects, developed a single-base editing tool with high efficiency and accuracy, which overcame the major challenge in medical applications to a certain extent. Moreover, his achievements in therapeutic studies using mouse models of human diseases provide support for therapeutic applications. Additionally, C-CRISPR technology significantly improved the efficiency of gene editing, and developed F0 generation of primates bearing gene knockout, which made important contributions to the rapid establishment of primate disease models.

Zuo is a recipient of many awards. Single-base gene editing caused substantial off-target effects, and its optimization was selected as the "Top Ten Advances in Life Sciences in China 2019". The rational engineering of cytosine base editor that enables to minimize of the off-target effect of DNA and RNA and maintains high targeting activity was selected as one of the "2020 Major Scientific Discoveries" by the Chinese Academy of Agricultural Sciences and received the "Major Achievement Award" by the Institute of Genomic Research 2021. The one-step production of complete knockout animals received the "Merit Award" at the 2017 ISSCR annual meeting. Recently, he has published a large number of articles in gene editing top journals including  Science ,  Nature, etc.

团队研究方向:

团队主要开展新型基因编辑技术的研发与应用研究。通过提高基因编辑工具的效率和精准度，减少其脱靶效应，扩大其应用范围。推动基因编辑技术在医学应用的安全性评价体系建设，不断探索基因编辑技术在生猪育种领域的创新应用，创制育种新材料。

The team focuses on the development and application of novel gene editing technologies. The improved efficiency and accuracy of gene editing tools reduce their off-target effects and expand their application scope. The achievements promoted the construction of a safety assessment system of gene editing technology in both medical and biological breeding fields, enhanced the application of gene editing technology in the pig breeding field, and created new breeding materials.

研究进展：

（1）建立了“一步法”获得基因完全敲除动物的技术体系，有效缩短基因编辑动物的创制时间。(Zuo et. al., Cell Research, 2017)

Established a "one-step" technology system to generate complete knockout animals and effectively shorten the time of producing genetic animals.

（2）建立了全染色体敲除技术，为开发染色体缺失的动物模型提供了一种新方法，也为涉及人类非整倍体染色体疾病提供了潜在的治疗策略。(Zuo et. al., Genome Biology, 2017)

Established a whole chromosome knockout technique that offers a new approach to developing animal models with chromosome deletions, and a potential therapeutic strategy for human aneuploidy diseases involving additional chromosomes.

（3）建立了GOTI的新型脱靶检测技术，可检测之前手段无法发现的完全随机的脱靶位点，显著提高基因编辑技术的脱靶检测灵敏性，为基因编辑工具的安全性评估带来了突破性的新工具，有望成为新的行业检测标准。(Zuo et.al., Science, 2019; Zuo et.al., Nature Protocols, 2020)

Developed “GOTI”, a novel off-target detection technology that can detect completely random off-target which is undetectable by previous means. Moreover, this strategy significantly improved the sensitivity of off-target detection for gene editing technology, brought a breakthrough new tool for safety assessment of gene editing tools, and potentially became a new industry standard for detection.

（4）开发新一代高保真基因编辑技术，可进行高效率和高保真度的C-G单碱基编辑，有效降低脱靶效率。(Zuo et. al., Nature methods. 2020；Yuan et. al., Nature Communications,2021)

Designed a new version of high-fidelity gene editing technology that allows for high-efficiency and high-fidelity C-G single-base editing, effectively reducing off-target efficiency.

研究成果：

1. Wei,Y.*, Li,Z.*, Xu,K.*, Feng,H.*, Xie,L.*, Li,D., Zuo,Z., Zhang,M.#, Xu,C.#, Yang,H.#, Zuo,E.#. Mitochondrial base editor DdCBE causes substantial DNA off-target editing in nuclear genome of embryos[J]. Cell Discovery, 2022; 8(27): 1-4.

2. Wei,Y.*, Xu,C.*, Feng,H.*, Xu,K.*, Li,Z.*, Hu,J., Zhou,L., Wei,Y., Zuo,Z., Zuo, E., Li,W.#, Yang,H.#, Zhang,M.#. Human cleaving embryos enable efficient mitochondrial base-editing with DdCBE[J]. Cell Discovery, 2022; 8(7): 1-4

3. Gu,X.*, Hu,X.*, Wang,D.*, Xu,Z.,  Wang,F., Li,D.,  Li, G., Yang,H.,Li,H.#, Zuo,E.# & Shu,Y.#, （2022）.Treatment of autosomal recessive hearing loss via in vivo CRISPR/Cas9-mediated optimized homology-directed repair in mice.Cell Research, volume 32, pages 699–702

4. Sameh A.Abdelnour,Xie,L., Abdallah A. Hassanin, Zuo,E.#and  Lu,Y#.(2021)The Potential of CRISPR/Cas9 Gene Editing as a Treatment Strategy for Inherited. Diseases.Frontiers in Cell and Developmental Biology.2021,9

5. Yuan,T.*, Yan,N.*, Fei,T.*, Zheng,J.*, Meng,J.*, Li,N.*, Liu,J.*, Zhang,H., Xie,L., Ying,W., Li,D., Shi,L., Sun,Y.,Li,Y., Li,Y., Sun,Y.# and Zuo,E.#.(2021). Optimization of C-to-G base editors with sequence context preference predictable by machine learning methods.Nature Communications: 12:4902

6. Xue,Y.*, Hu,X.*,Wang,D.*, Li,D.*,Li,Y.,Wang,F.,Huang,M., Gu,X., Xu,Z., Zhou,J., Wang,J., Chai,R., Shen,J., Chen,Z., Li,G., Yang,H., Li,H.#, Zuo,E.# and Shu,Y.#. (2021).Gene editing in a Myo6 semi-dominant mouse model rescues auditory function Author links open overlay panel .Molecular Therapy. DOI: 10.1016/j.ymthe.2021.06.015

7. Zhang,J.*, E,M.Khazalwa.*, H, M.Abkallo., Zhou,Y., Nie,X., Ruan,J., Zhao,C., Wang,J., Xu,J., Li.X., Zhao,S., Zuo,E.#, L,Steinaa#.and Xie,S.#.(2021).The Advancements, Challenges and Future Implications of the CRISPR/Cas9 System in Swine Research.Journal of Genetics and Genomics:48(5).347-360.

8. Wei,Y.*, Zhou, Y.*, Liu,Y.*, Ying,W., Lv,R., Zhao,Q.,  Zhou,H., Zuo,E.#,  Sun,Y.#, Yang,H.# and Zhou,C,#. (2021). Indiscriminate ssDNA cleavage activity of CRISPR-Cas12a induces no detectable off-target effects in mouse embryos.Protein & Cell .12,741–745.  DOI: 10.1007/s13238-021-00824-z

9. Huang, X.*, Lv, J.,*, Li, Y.*, Mao, S., Li, Z., Jing, Z., Sun, Y., Zhang,X., Shen, S., Wang, X., Di, M., Ge, J., Huang, X., Zuo,E.# and Chi, T.#.（2020）. Programmable C-to-U RNA editing using the human APOBEC3A deaminase .The EMBO Journal:39(22):e104741.

10. Zuo,E.*, Sun,Y. *, Wei,Wu.*, Yuan ,T.*, Ying,W., Sun,H., Yuan,L., Lars M. Steinmetz # , Li,Y.# and Yang,H.#.(2020).GOTI, a method to identify genome-wide off-target effects of genome editing in mouse embryos.Natrue Protocols:15.3009–3029.

11. Lee,S.*, Ding,N.*, Sun,Y., Yuan,T., Li,J., Yuan,Q., Liu,L.,Yang,J.,Wang,Q., Anatoly B. Kolomeisky, Isaac B. Hilton, Zuo,E.# and Gao,X.#. (2020).Single C-to-T substitution using engineered  APOBEC3G-nCas9 base editors with minimum  genome- and transcriptome-wide off-target effects.Science Advance:6（29）.

12. Zuo,E.*#, Sun,Y.*, Yuan ,T.*?, He,B.*?, Zhou,C.*?, Ying,W., Liu,L., Wei?,W., Zeng,R., Li,Y.# and Yang,H.#.(2020).A rationally engineered cytosine base editor retains high on-target activity while reducing both DNA and RNA off-target effects.Nature Methods:17(6):600–604.

13.  Lin X.*, Chen H.*, Lu Y.*, Hong S.*, Hu X.*, Gao Y., Lai L., Li J., Wang Z., Ying W., Ma L., Wang N., Zuo,E.#, Yang H.# and Chen W. #.(2020).Base editing-mediated splicing correction therapy for spinal muscular atrophy. Cell Research:0:1-3. 30(6).

14. Deng K.*, Feng W.*, Liu X.*, Su X., Zuo,E., Du S., Huang Y., Shi D. # and Lu,F. # .(2020).Anti-silencing Factor 1A is Associated with Genome Stability Maintenance of Mouse Preimplantation Embryos.Biology of Reproduction:102(4),817-827.

15. Li J. *, Lin X. *, Tang C. *, Lu Y. *, Hu X. *, Zuo,E., Li H., Ying W., Sun Y. , Lai L., Chen H., Guo X., Zhang Q., Wu S., Zhou C., Shen X., Wang Q., Lin ., Ma L., Wang N.,Ad.Krainer, Shi L.#, Yang H.# and Chen W.#.(2020) .Disruption of splicing-regulatory elements using CRISPR/Cas9 to rescue spinal muscular atrophy in human iPSCs and mice.National Science Review:7(1),92-101.

16. Zhao, X., Wei, W., Pan,H., Nie,J., Chen,D., Zhang,P., Chen, F., Fu, Q,. Zuo, E.#, Lu, Y.# and Zhang, M.#. (2019). Identification of the Sex of Pre-implantation Mouse Embryos Using a Marked Y Chromosome and CRISPR/Cas9. SCIENTIFIC REPORTS:9: 14315.

17. Li,J.* , Hong,S.*, Chen,W.#, Zuo,E.# and Yang,H.#.(2019) . Advances in detecting and reducing off-target effects generated by CRISPR-mediated genome editing.Journal of Genetics and Genomics:46(11),513-521.

18. Wang, X.*, Kang, J.*, Wei, L.*, Yang, X.*, Sun, H., Yang, S., Lu, L., Yang, M., Bai, M., Chen, Y., Long, J., Li, N., Li, D., Huang, J., Lei, M., Shao, Z., Yuan, W.#, Zuo, E.#, Lu, K. #, Liu, M.# and Li, J#. (2019). PHF7 is a novel histone H2A E3 ligase prior to histone-to-protamine exchange during spermiogenesis. Development:146（13） dev.175547.

19. Zhou, C.*, Sun, Y.*, Yan, R.*, Liu, Y.*, Zuo, E.*, Gu, C., Han, L., Wei, Y., Hu, X., Zeng, R., Li, Y.#, Zhou, H.#, Guo, F.# and Yang, H.# .(2019).Off-target RNA mutation induced by DNA base editing and its elimination by mutagenesis. Nature:571, 275–278.

20. Zuo, E.*, Sun, Y.*, Wei, W.*, Yuan, T.*, Ying, W., Sun, H., Yuan, L., Steinmetz, L. M.#, Li, Y.# and Yang, H#.(2019). Cytosine base editor generates substantial off-target single-nucleotide variants in mouse embryos. Science:364（6437）, 289-292.

21. Zuo, E.*, Huo, X.*, Yao, X.*, Hu, X.*, Sun, Y.*, Yin, J*., He, B., Wang, X., Shi, L., Ping, J., Wei, Y., Ying, W., Wei, W., Liu, W., Tang, C., Li, Y., Hu, J.# and Yang, H.#. (2017).CRISPR/Cas9-mediated targeted chromosome elimination. Genome Biology:18:224.

22. Zuo, E.*, Cai, Y. J.*, Li, K.*, Wei, Y.*, Wang, B. A.*, Sun, Y.*, Liu, Z., Liu, J., Hu, X., Wei, W., Huo, X., Shi, L., Tang, C., Liang, D., Wang, Y., Nie, Y. H., Zhang, C. C., Yao, X., Wang, X., Zhou, C., Ying, W., Wang, Q., Chen, R. C., Shen, Q., Xu, G. L., Li, J., Sun, Q., Xiong#, Z. Q.# and Yang, H#.(2017).One-step generation of complete gene knockout mice and monkeys by CRISPR/Cas9-mediated gene editing with multiple sgRNAs. Cell Research:27, 933-945.

23. Wang,L. *, Li,M. *, Qu, C.,Miao,W., Yin,Q., Liao,J., Cao,H., Huang,M., Wang,K. Zuo,E. , Peng,G., Zhang,S., Chen,G., Li,Q., Tang,K., Yu, Q., Li,Z., Catherine CL Wong, Xu,G., Jing, N.,Yu,X.,# and Li,J.#.(2017).CRISPR-Cas9-mediated genome editing in one blastomere of two-cell embryos reveals a novel Tet3 function in regulating neocortical development.Cell Research:1-15.

24. Zuo, E. *, Yang, X.#, Lu, Y., Xie, L., Shang, J., Li, D., Yang, H., Hu, L., Zhao, H., Lu, S., Lu, K.#.(2015). ZPAC is required for normal spermatogenesis in mice. Mol. Reprod：Dev. 82(10): 747-755.

25. Zhang, M.*, Zhou, H., Zheng, C. ,Xiao, J. , Zuo, E., Liu, W., Xie, D.,Shi, Y.,Wu, C., Wang, H. , Li, D. & Li, J .#.(2014).The Roles of Testicular C-kit Positive Cells in De novo Morphogenesis of Testis. SCIENTIFIC REPORTS：4 : 5936.

26. Liu,H.*, Lv,P., Zhu,X., Wang,X., Yang,X., Zuo,E., Lu,Y., Lu, S., Lu,K.#.(2014).In vitro development of porcine transgenic nuclear-transferred embryos derived from newborn Guangxi Bama mini-pig kidney fibroblasts.In Vitro Cell.Dev.Biol.—Animal：50:811–821.