季泉江 - 上海科技大学 - 物质科学与技术学院

个人简介

Bio: Associate Professor, ShanghaiTech University, 2021-current; Assistant Professor, ShanghaiTech University, 2016-2020; Postdoc., University of California, Berkeley (Advisor: Prof. Michelle Chang), 2014-2016; Ph.D., University of Chicago (Advisor: Prof. Chuan He), 2009-2014; B.S., Nanjing University, 2005-2009. Awards: Chinese Chemical Society Award for Young Chemists, 2022; Lingang Laboratory Qiusuo Distinguished Young Scholar, 2022； NSFC Excellent Young Scholar，2019; Shanghai Science and Technology Committee Rising-Star Program，2019; Young Overseas High-Level Talents Introduction Plan, 2016; Camille and Henry Dreyfus Postdoctoral Fellowship, 2015; Chinese Government Award for Outstanding Self-Financed Students Abroad, 2013; The Everett E Gilbert Memorial Prize, 2012.

研究领域

Advances in the understanding and development of CRISPR-Cas systems have revolutionized the gene editing methods in biology and medicine. However, the imperfect properties of current CRISPR-Cas technology, such as a high off-target rate, a strict PAM requirement, high cell toxicity, and large gene size, restrict its diverse applications. We aim to discover, characterize, and engineer new CRISPR-Cas systems with superior properties compared with current CRISPR-Cas systems. In addition, we leverage different CRISPR-Cas systems to develop rapid and efficient gene editing tools in major human pathogens to facilitate fundamental understanding of infection and drug-resistance mechanisms. Finally, we aim to develop CRISPR-based antimicrobial strategies to counter infections caused by drug-resistant human pathogens.

近期论文

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Wu, Z.#, Liu, D.#, Pan, D.#, Yu, H., Shi, J., Ma, J., Fu, W., Wang, Z., Zheng, Z., Qu, Y., Li, F., Chen, W., Huang, X., Shen, H.*, Ji, Q.* (2023) Structure and engineering of miniature Acidibacillus sulfuroxidans Cas12f1. Nature Catalysis doi: 10.1038/s41929-023-00995-4 (accepted). Chen, W.#, Ma, J.#, Wu, Z., Wang, Z., Zhang, H., Fu, W., Pan, D., Shi, J., Ji, Q.* (2023) Cas12n nucleases, early evolutionary intermediates of type V CRISPR, comprise a distinct family of miniature genome editors. Molecular Cell 83: 1-13. Gründling, A.*, Ji, Q.* (2023) Introduction of a CRISPR-nCas9 gene-targeting plasmid into Staphylococcus aureus for gene disruption. Cold Spring Harbor Protocols doi: 10.1101/pdb.prot107925. Gründling, A.*, Ji, Q.* (2023) Identification of editable sites, spacer oligonucletide design, generation of the gene-targeting CRISPR-nCas9 plasmid for gene disruption in Staphylococcus aureus using the CRISPR-nCas9 and cytidine deaminase system. Cold Spring Harbor Protocols doi: 10.1101/pdb.prot107924. Gründling, A.*, Ji, Q.*, Salipante, S.J.* (2023) Using CRISPR-Cas9-based methods for genome editing in Staphylococcus aureus. Cold Spring Harbor Protocols doi: 10.1101/pdb.top107919. Li, X., Zhang, G., Huang, S., Liu, Y., Tang, J., Zhong, M., Wang, X., Sun, W., Yao, Y., Ji, Q., Wang, X., Liu, J., Zhu, S., Huang, X.* (2023) Development of a versatile nuclease prime editor with upgraded precision. Nature Communications 14: 305. Wang, Z.#, Zhang, Y.#, Chen, C., Zhu, R., Jiang, J., Weng, T.C., Ji, Q.*, Huang, Y.*, Fang, C.*, Liu, W.* (2023) Mapping the complete photocycle that powers a large stokes shift red fluorescent protein. Angew Chem 62: e202212209. Wang, Yuj., Wang, Ya., Pan, D., Yu, H., Zhang, Y., Chen, W., Li, F., Wu, Z.*, Ji, Q.* (2022) Guide RNA engineering enables efficient CRISPR editing with a miniature Syntrophomonas palmitatica Cas12f1 nuclease. Cell Reports 40: 111418. Wang, Z., Wang, Yu, Wang, Yuj., Chen, W., Ji, Q.* (2022) CRISPR/Cpf1-mediated multiplex and large-fragment gene editing in Staphylococcus aureus. ACS Synthetic Biology 11: 3049-3057. Zhang, Y.#, Chen, W.#, Liu, D.#, Liu, Y., Wu, Z., Li, J., Zhang, S.Y.*, Ji, Q.* (2022) Molecular basis for cell-wall recycling regulation by transcriptional repressor MurR in Escherichia coli. Nucleic Acids Research 50: 5948-5960. Zhang, H., Zhang, Y., Wang, W.X., Chen, W.Z., Zhang, X., Huang, X., Chen, W.*, Ji, Q.* (2022) PAM-expanded Streptococcus thermophilus Cas9 C-to-T and C-to-G base editors for programmable base editing in mycobacteria. Engineering 15: 67-77. Huang, X., Li, X., An, H., Wang, J., Ding, M., Wang, L., Li, L., Ji, Q., Qu, F., Wang, H., Xu, Y., Lu, X., He, Y., Zhang, J.R.* (2022) Capsule type defines the capability of Klebsiella pneumoniae in evading Kupffer cell capture in the liver. PLoS Pathogens 18: e1010693. Zhang, G.#, Liu, Y.#, Huang S.#, Qu, S., Cheng, D., Yao, Y., Ji, Q., Wang, X.*, Huang, X.*, Liu, J.* (2022) Enhancement of prime editing via xrRNA motif-joined pegRNA. Nature Communications 13: 1856. Li, X., Wang, X., Sun, W., Huang, S., Zhong, M., Yao, Y., Ji, Q., Huang, X.* (2022) Enhancing prime editing efficiency by modified pegRNA with RNA G-quadruplexes. Journal of Molecular Cell Biology 14: mjac022. Yu, L., Cao, Q., Chen, W., Yang, N., Yang, C.G., Ji, Q., Wu, M., Bae, T. Lan, L.* (2022) A novel copper-sensing two-component system for inducing Dsb gene expression in bacteria. Science Bulletin 67: 198-212. Wu, Z., Zhang, Y., Yu, H., Pan, D., Wang, Yuj., Wang, Ya., Li, F., Liu, C., Nan, H., Chen, W., Ji, Q.* (2021) Programmed genome editing by a miniature CRISPR-Cas12f nuclease. Nature Chemical Biology 17: 1132-1138. Chen, W.#, Ren, Z.#, Tang, N., Chai, G., Zhang, H., Zhang, Y., Ma, J., Wu, Z., Shen, X., Huang, X., Luo, G.Z.*, Ji, Q.* (2021) Targeted genetic screening in bacteria with a Cas12k-guided transposase. Cell Reports 36: 109635. Liu, Y., Chen, Y., Dang, L., Liu, Y., Huang, S., Wu, S., Ma, P., Jiang, H., Li, Y., Pan, Y., Wei, Y., Ma, X., Liu, M., Ji, Q., Chi, T., Huang, X.*, Wang, X.*, Zhou, F.* (2021) EasyCatch, a conventient, sensitive and specific CRISPR detection system for cancer gene mutations. Molecular Cancer 20: 157. Zhang, Y., Zhang, H., Xu, X., Wang, Yuj, Chen, W., Wang, Ya., Wu, Z., Tang, N., Wang, Yu, Zhao, S., Gan, J.*, Ji, Q.* (2020) Catalytic-state structure and engineering of Streptococcus thermophilus Cas9. Nature Catalysis 3: 813-823. Yu, H.#, Wu, Z.#, Chen, X., Ji, Q.*, Tao, S.* (2020) CRISPR-CBEI: a designing and analyzing tool kit for cytosine base editor-mediated gene inactivation. mSystems 5: e00350-20. Wang, Y.*, Wang, Z., Ji, Q.* (2020) CRISPR-Cas9-based genome editing and cytidine base editing in Acinetobacter baumannii. STAR Protocols DOI: 10.1016/j.xpro.2020.100025. Pi, Y., Chen, W., Ji, Q.* (2020) Structural basis of Staphylococcus aureus surface protein SdrC. Biochemistry 59: 1465-1469. Zhang, Y., Zhang, H., Wang, Z., Wu, Z., Wang, Y., Tang, N., Xu, X., Zhao, S., Chen, W.*, Ji, Q.* (2020) Programmable adenine deamination in bacteria using a Cas9-adenine-deaminase fusion. Chemical Science 11: 1657-1664. Wu, Z., Wang, Y., Zhang, Y., Chen, W., Wang, Y., Ji, Q.* (2020) Strategies for developing CRISPR-based gene editing methods in bacteria. Small Methods 4: 1900560. Chen, W., Zhang, H., Zhang, Y., Wang, Y., Gan, J.*, Ji, Q.* (2019) Molecular basis for the PAM expansion and fidelity enhancement of an evolved Cas9 nuclease. PLoS Biology 17: e3000496. Wang, Y., Wang, Z., Chen, Y., Hua, X., Yu, Y., Ji, Q.* (2019) A highly efficient CRISPR-Cas9-based genome engineering platform in Acinetobacter baumannii toward the understanding of H2O2-sensing mechanism of OxyR. Cell Chemical Biology 26: 1732-42. Zhang, Y., Sun, X., Qian, Y., Yi, H., Song, K., Zhu, H., Zonta, F., Chen, W., Ji, Q., Miersch, S, Sidhu, S.S.*, Wu, D.* (2019) A potent anti-SpuE antibodyallosterically inhibits type III secretion system and attenuates virulence of Pseudomonas aeruginosa. Journal of Molecular Biology 431:4882-4896. Fu, T., Liu, L., Yang, Q.L., Wang, Y., Xu, P., Zhang, L., Liu, S., Dai, Q., Ji, Q., Xu, G.L., He, C., Luo, C.*, Zhang, L.* (2019) Thymine DNA glycosylase recognizes the geometry alteration of minor grooves induced by 5-formylcytosine and 5-carboxylcytosine. Chemical Science 10: 7407-17. He, T., Wang, R., Liu, D., Walsh, T.R., Zhang, R., Lv, Y., Ke, Y., Ji, Q., Wei, R., Liu, Z., Shen, Y., Wang, G., Sun, L., Lei, L., Lv, Z., Li, Y., Pang, M., Wang, L., Sun, Q., Fu, Y., Song, H., Hao, Y., Shen, Z., Wang, S., Chen, G., Wu, C., Shen, J., Wang, Y. (2019) Emergence of plasmid-mediated high-level tigecycline resistance genes in animals and humans. Nature Microbiology 4: 1450-6. Sun, Q.#, Wang, Y.#, Dong, N., Shen, L., Zhou, H., Hu, Y., Gu, D., Chen, S., Zhang, R.*, Ji, Q.* (2019) Application of CRISPR/Cas9-based genome editing in studying the mechanism of pandrug resistance in Klebsiella pneumoniae. Antimicrobial Agents and Chemotherapy 63: e00113-19. Wang, Y., Wang, S., Chen, W., Song, L., Shen, Z., Yu, F., Li, M., Ji, Q.*(2018) Precise and efficient genome editing in Klebsiella pneumoniae using CRISPR-Cas9 and CRISPR-assisted cytidine deaminase. Applied and Environmental Microbiology 84: e01834-18. Chen, W., Zhang, Y., Zhang, Y., Pi, Y., Gu, T., Song, L., Wang, Y., Ji, Q.* (2018) CRISPR/Cas9-based genome editing in Pseudomonas aeruginosa and cytidine deaminase-mediated base editing in Pseudomonas species. iScience 6: 222-31. Wei, W.#, Zhang, Y.#, Gao, R., Li, J., Xu, Y., Wang, S., Ji, Q.*, Feng, Y.* (2018) Crystal structure and acetylation of BioQ suggests a novel regulatory switch for biotin biosynthesis in Mycobacterium smegmatis. Molecular Microbiology 109: 642-62. Song, L., Zhang, Y., Chen, W., Gu, T., Zhang, S.Y., Ji, Q.* (2018) Mechanistic insights into staphylopine-mediated metal acquisition. PNAS 115: 3942-7. Gu, T.#, Zhao, S.#, Pi, Y., Chen, W., Chen, C., Liu, Q., Li, M., Han, D.*, Ji, Q.* (2018) Highly efficient base editing in Staphylococcus aureus using an engineered CRISPR RNA-guided cytidine deaminase. Chemical Science 9: 3248-53. Chen, W., Zhang, Y., Yeo, W.S., Bae, T., Ji, Q.* (2017) Rapid and efficient genome editing in Staphylococcus aureus by using an engineered CRISPR/Cas9 system. JACS 139: 3790-5.