刘朋朋，南方科技大学医学院，助理教授，博士生导师。多年来致力于蛋白质工程以及进化技术开发新型高效安全的基因组编辑工具，并应用其实现基因组的高效精准编辑。优化改造核酸酶(Nuclease)，单碱基编辑(Base Editor, BE)和先导编辑工具(Prime Editor, PE)，以实现在多种细胞包括CD34+造血干细胞，NK细胞以及原始T细胞中的高效精准编辑，治疗包括β-地中海贫血、镰状细胞病和HIV在内的多种疾病；同时优化开发包括ex vivo RNP， LNP-mRNA/circular RNA ex vivo和体内投递技术。此外，还开发了一系列脱靶检测工具以评估各种基因编辑工具在临床应用过程中的安全性。近些年相关的研究已经在Nature Biotechnology、Nature Methods、Nature Cell Biology、Nature Medicine、Nature Communications和 Nucleic acids research等高水平期刊发表论文30余篇，以第一作者以及通讯作者身份（含共同）发表论文 11 篇 （Nature Biotechnology, 2024. Nucleic acids research，2023. Nature Methods, 2023. Nature Communications, 2022, Nature Communications, 2021. Nucleic acids research, 2019. Nature Communications, 2018. Cell Research, 2015. 2014, 2011.）。累计SCI影响因子大于500，Google Scholar累计引用次数大于3000, H-Index 24。同时以主要发明人，拥有7项专利技术。
i. AI辅助蛋白质设计与进化：
基于人工智能从头设计蛋白质，并利用不同蛋白表达体系进行蛋白迭代定向进化，以获得活性更高/特异性更强的蛋白质，用于进一步的基因组工程治疗应用。
ii. 开发高效特异的基因编辑工具递送方法：
开发基于 mRNA-LNP（脂质纳米颗粒）以及eVLP-RNP（核糖核蛋白-工程化微囊泡）的递送系统，用于ex vivo 以及 in vivo的基因治疗和细胞治疗。
iii. 开发更灵敏的体外和体内脱靶检测方法：
利用湿实验方法和生物信息学分析，在体外、细胞和体内检测 CRISPR/Cas 核酸酶、碱基编辑器和先导编辑器的脱靶效应。
2015.8-2022.4 麻省医学院，癌细胞生物学，博士后
2008.9-2014.7 北京大学，细胞生物学，博士
2004.9-2008.7 郑州大学，生物技术，学士
2024.11-至今 南方科技大学，医学院，助理教授，博导
2022.5-2024.11麻省医学院，癌细胞生物学，讲师
2019年以来担任Nature Methods 、Nature Biotechnology、Nature Communications， NAR 等杂志审稿人。
1. Exome sequencing reveals the genetic architecture of non-syndromic orofacial clefts and identifies BOC as a novel causal gene. Qing He, Min Yu, Yizhu Xu, Yuhua Jiao, Xuqin Liang, Wenbin Huang, Yuxia Hou, Zhanping Ren, Huimei Huang, Huaxiang Zhao, Pengpeng Liu, Yi Ding. (Advanced Science. 2025)
2. in vivo prime editing rescues photoreceptor degeneration in nonsense mutant retinitis pigmentosa. Yidian Fu, Xiaoyu He, Liang Ma, Xin D. Gao, Pengpeng Liu , Hanhan Shi, Peiwei Chai, Shengfang Ge, Renbing Jia, David R. Liu, Xianqun Fan, Zhi Yang (Nature Communications. 2025)
3. Gene editing without ex vivo culture evades genotoxicity in human hematopoietic stem cells. Jing Zeng1, My Anh Nguyen1, Pengpeng Liu1, Lucas Ferreira da Silva1,3, Linda Y. Lin1, David G. Justus4, Karl Petri3, Vikram Pattanayak3, Kendell Clement3, Shaina N. Porter5, Archana Verma1, Nola R. Neri1, Tolulope Rosanwo1, Marioara-Felicia Ciuculescu6, Daniela Abriss6, Esther Mintzer2, Stacy A. Maitland2, David A. Williams1, Lihua Julie Zhu7, Shondra M. Pruett-Miller5, Luca Pinello3, J. Keith Joung3, John P. Manis1, Myriam Armant6, Danilo Pellin1, Christian Brendel1, Scot A. Wolfe2, Daniel E. Bauer1,8,* (Cell stem cell, 2024)
4. Improving specific and efficient base editing with Cas-embedded eA3A ribonucleoprotein complexes. Jeongmin Lee, Jing Zeng, Pengpeng Liu, Karthikeyan Ponnienselvan , Daniel E. Bauer, Nese Kurt Yilmaz, Scot A. Wolfe, Celia A. Schiffer. Nucleic acids research. (2024)
5. Increasing intracellular dNTP levels improves prime editing efficiency. Pengpeng Liu, Karthikeyan Ponnienselvan, Thomas Nyalile, Sarah Oikemus, Anya Joint, Karen Kelly, Dongsheng Guo, Zexiang Chen, Jeong Min Lee, Charles Emerson, Nathan D. Lawson, Jonathan K. Watts, Erik J. Sontheimer, Jeremy Luban, Scot A. Wolfe. (2024) (First author) (Nature Biotechnology, 2024).
6. Transcriptional suppression of sphingolipid catabolism controls pathogen resistance in
C. elegans. Mohamad A. Nasrallah, Nicholas D. Peterson, Elizabeth S. Szumel, Pengpeng Liu,
Amanda L. Page, Samantha Y. Tse, Khursheed A. Wani, Claire E. Tocheny, Read Pukkila-Worley. PLoS Pathog 19(10): e1011730. (2023)
7. Reducing the inherent auto-inhibition interaction within the pegRNA enhances prime editing efficiency. Karthikeyan Ponnienselvan, Pengpeng Liu, Thomas Nyalile, Sarah Oikemus, Nathan Lawson, Jeremy Luban, Scot Wolfe. Nucleic acids research. (2023) (Co-First author)
8. Genome-wide Profiling of Prime editor off-target sites in vitro and in vivo using PE-tag. Shun-Qing Liang, Pengpeng Liu2*, Karthikeyan Ponnienselvan, Sneha Suresh, Zexiang Chen, Christian Kramme, Pranam Chatterjee, Lihua Julie Zhu, Erik J. Sontheimer, Wen Xue*, Scot A. Wolfe*. Nature Methods. (2023) https://doi.org/10.1038/s41592-023-01859-2 (Co-First author and Co-Corresponding author)
9. Optimization of NLS Composition Improves CRISPR-Cas12a Editing Rates in Human Primary Cells. Kevin Luk, Pengpeng Liu,Jing Zeng, Yetao Wang, Stacy A. Maitland, Feston Idrizi, Karthikeyan Ponnienselvan, Lihua Julie Zhu, Jeremy Luban, Daniel E. Bauer, and Scot A. Wolfe. GEN Biotechology. 1: 271-284 (2022) (Co-First author)
10. Enhancing Prime Editing Efficiency and Flexibility with Tethered and Split pegRNAs. Ying Feng, Siyuan Liu, Qiqin Mo, Xiao Xiao, Pengpeng Liu, Hanhui Ma. Protein & Cell. (2022).
11. Efficient Homology-Directed Repair with Circular Single-Stranded DNA Donors. Iyer S, Mir A, Vega-Badillo J, Roscoe BP, Ibraheim R, Zhu LJ, Lee J, Liu P, Luk K, Mintzer E, Guo D, Soares de Brito J, Emerson CP Jr, Zamore PD, Sontheimer EJ, Wolfe SA. CRISPR J. (2022)
12. Adenine Base Editing In Vivo with a Single Adeno-Associated Virus Vector. Han Zhang, Nathan Bamidele, Pengpeng Liu, Ogooluwa Ojelabi, Xin D. Gao, Tomás Rodriguez, Haoyang Cheng, Karen Kelly, Jonathan K. Watts, Jun Xie, Guangping Gao, Scot A. Wolfe, Wen Xue, and Erik J. Sontheimer. GEN Biotechology. 1: 285-299 (2022)
13. Genome-wide detection of CRISPR editing in vivo using GUIDE-tag. Shun-Qing Liang, Pengpeng Liu, Jordan L. Smith, Esther Mintzer, Stacy Maitland, Xiaolong Dong, Qiyuan Yang, Jonathan Lee, Cole M. Haynes, Lihua Julie. Zhu, Jonathan K. Watts, Erik J. Sontheimer, Scot A. Wolfe*, Wen Xue*. Nature Communications. 13:437-450 (2022) (Co-First author)
14. A flexible split prime editor using truncated reverse transcriptase improves dual AAV delivery in mouse liver. Chunwei Zheng, Shun-Qing Liang, Bin Liu, Pengpeng Liu, Suet-Yan Kwan, Scot A Wolfe, Wen Xue. Molecular Therapy. 30(3):1343-1351 (2022)
15. mtDNA replication in dysfunctional mitochondria promotes deleterious heteroplasmy via the UPRmt. Qiyuan Yang, Pengpeng Liu, Nadine S Anderson, Tomer Shpilka, YunGuang Du, Nandhitha Uma Naresh, Kevin Luk, Josh Lavelle, Rilee D Zeinert, Peter Chien, Scot A Wolfe, Cole M Haynes. Nature Cell Biology. 24(2):181-193 (2022)
16. ATF-4 and hydrogen sulfide signalling mediate longevity in response to inhibition of translation or mTORC1. Cyril Statzer, Jin Meng, Richard Venz, Monet Bland, Stacey Robida-Stubbs, Krina Patel, Dunja Petrovic, Raffaella Emsley, Pengpeng Liu, Ianessa Morantte, Cole Haynes, William Mair, Alban Longchamp, Milos Filipovic, Keith Blackwell, Collin Ewald. Nature Communications. 13:967-972 (2022)
17. The KRAB Domain‐Containing Protein ZFP961 Represses Adipose Thermogenesis and Energy Expenditure through Interaction with PPARα. Lei Huang, Pengpeng Liu, Qiyuan Yang, YongXu Wang. Advanced Science. 9(2):e2102949 (2021)
18. 5′-Modifications improve potency and efficacy of DNA donors for precision genome editing. Krishna S Ghanta, Zexiang Chen, Aamir Mir, Gregoriy A Dokshin, Pranathi M Krishnamurthy, Yeonsoo Yoon, Judith Gallant, Ping Xu, Xiao-Ou Zhang, Ahmet Rasit Ozturk, Masahiro Shin, Feston Idrizi, Pengpeng Liu, Hassan Gneid, Alireza Edraki, Nathan D Lawson, Jaime A Rivera-Pérez, Erik J Sontheimer, Jonathan K Watts, Craig C Mello. Elife. 10:e72216 (2021)
19. Improved prime editors enable pathogenic allele correction and cancer modelling in adult mice. Pengpeng Liu, Shun-Qing Liang, Chunwei Zheng, Esther Mintzer, Yan G Zhao, Karthikeyan Ponnienselvan, Aamir Mir, Erik J Sontheimer, Guangping Gao, Terence R Flotte, Scot A Wolfe, Wen Xue. Nature Communications. 12(1):1-13 (2021). (First author)
20. UPRmt scales mitochondrial network expansion with protein synthesis via mitochondrial import in Caenorhabditis elegans. Tomer Shpilka, YunGuang Du, Qiyuan Yang, Andrew Melber, Nandhitha Uma Naresh, Joshua Lavelle, Sookyung Kim, Pengpeng Liu, Hilla Weidberg, Rui Li, Jun Yu, Lihua Julie Zhu, Lara Strittmatter, Cole M Haynes. Nat Communications. 12(3): 1-11 (2021)
21. Genome-wide detection and analysis of CRISPR-Cas off-targets. Tomás C Rodríguez, Sina Dadafarin, Henry E Pratt, PengPeng Liu, Nadia Amrani, Lihua Julie Zhu. Progress in molecular biology and translational science. 181:31-43 (2021)
22. Innate immunity in the C. elegans intestine is programmed by a neuronal regulator of AWC olfactory neuron development. Kyle J Foster, Hilary K Cheesman, Pengpeng Liu, Nicholas D Peterson, Sarah M Anderson, Read Pukkila-Worley. Cell reports. 31 (1): 107478 (2020)
23. Tissue-restricted genome editing in vivo specified by microRNA-repressible anti-CRISPR proteins. Jooyoung Lee, Haiwei Mou, Raed Ibraheim, Shun-Qing Liang, Pengpeng Liu, Wen Xue, Erik J Sontheimer. RNA. 25(11):1421-1431 (2019)
24. Enhanced Cas12a editing in mammalian cells and zebrafish. Pengpeng Liu, Kevin Luk, Masahiro Shin, Feston Idrizi, Samantha Kwok, Benjamin Roscoe, Esther Mintzer, Sneha Suresh, Kyle Morrison, Josias B Frazão, Mehmet Fatih Bolukbasi, Karthikeyan Ponnienselvan, Jeremy Luban, Lihua Julie Zhu, Nathan D Lawson, Scot A Wolfe. Nucleic acids research. 47 (8):4169-4180 (2019) (First author)
25. Highly efficient therapeutic gene editing of human hematopoietic stem cells. Yuxuan Wu, Jing Zeng, Benjamin P Roscoe, Pengpeng Liu, Qiuming Yao, Cicera R Lazzarotto, Kendell Clement, Mitchel A Cole, Kevin Luk, Cristina Baricordi, Anne H Shen, Chunyan Ren, Erica B Esrick, John P Manis, David M Dorfman, David A Williams, Alessandra Biffi, Carlo Brugnara, Luca Biasco, Christian Brendel, Luca Pinello, Shengdar Q Tsai, Scot A Wolfe, Daniel E Bauer. Nat Medicine. 25 (5):776-783 (2019)
26. Precise therapeutic gene correction by a simple nuclease-induced double-stranded break. Sukanya Iyer, Sneha Suresh, Dongsheng Guo, Katelyn Daman, Jennifer CJ Chen, Pengpeng Liu, Marina Zieger, Kevin Luk, Benjamin P Roscoe, Christian Mueller, Oliver D King, Charles P Emerson, Scot A Wolfe. Nature. 568 (7753):561-565 (2019)
27. The nuclear hormone receptor NHR-86 controls anti-pathogen responses in C. elegans. Nicholas D Peterson, Hilary K Cheesman, Pengpeng Liu, Sarah M Anderson, Kyle J Foster, Richa Chhaya, Paola Perrat, Jose Thekkiniath, Qiyuan Yang, Cole M Haynes, Read Pukkila-Worley. PLoS Genetics. 15(1):e1007935-46 (2019)
28. Potent Cas9 inhibition in bacterial and human cells by AcrIIC4 and AcrIIC5 anti-CRISPR proteins. Jooyoung Lee, Aamir Mir, Alireza Edraki, Bianca Garcia, Nadia Amrani, Hannah E Lou, Ildar Gainetdinov, April Pawluk, Raed Ibraheim, Xin D Gao, Pengpeng Liu, Alan R Davidson, Karen L Maxwell, Erik J Sontheimer. MBio. 9 (6):e02321-18 (2018)
29. NmeCas9 is an intrinsically high-fidelity genome-editing platform. Nadia Amrani, Xin D Gao, Pengpeng Liu, Alireza Edraki, Aamir Mir, Raed Ibraheim, Ankit Gupta, Kanae E Sasaki, Tong Wu, Paul D Donohoue, Alexander H Settle, Alexandra M Lied, Kyle McGovern, Chris K Fuller, Peter Cameron, Thomas G Fazzio, Lihua Julie Zhu, Scot A Wolfe, Erik J Sontheimer. Genome Biology. 19 (1):1-25 (2018)
30. Orthogonal Cas9–Cas9 chimeras provide a versatile platform for genome editing. Mehmet Fatih Bolukbasi, Pengpeng Liu, Kevin Luk, Samantha F Kwok, Ankit Gupta, Nadia Amrani, Erik J Sontheimer, Lihua Julie Zhu, Scot A Wolfe. Nature Communications. 9(1):1-12 (2018) (Co-First author)
31. Regulation of transcriptionally active genes via the catalytically inactive Cas9 in C. elegans and D. rerio. Lijiang Long, Hong Guo, Di Yao, Kai Xiong, Yongjun Li, Pengpeng Liu, Zuoyan Zhu, Dong Liu. Cell Research. 25:638–641 (2015) (Co-Corresponding author)
32. Heritable/conditional genome editing in C. elegans using a CRISPR-Cas9 feeding system. Pengpeng Liu, Lijiang Long, Kai Xiong, Bo Yu, Nannan Chang, Jing-Wei Xiong, Zuoyan Zhu, Dong Liu. Cell Research. 24:886–889 (2014) (First author)
33. mir-35 is involved in intestine cell G1/S transition and germ cell proliferation in C. elegans. Min Liu, Pengpeng Liu, Li Zhang, Qingchun Cai, Ge Gao, Wenxia Zhang, Zuoyan Zhu, Dong Liu, Qichang Fan. Cell Research. 21:1605–1618 (2011). (Co-First author)
Google scholar:
https://scholar.google.com/citations?hl=en&user=fE8Ph6UAAAAJ&pagesize=80&view_op=list_works
获得专利：
Enhanced bcl11a rnp/crispr delivery & editing using a 3xnls-cas9 (PCT/WIPO)
(https://patents.google.com/patent/WO2019213273A1/en)
Targeting bcl11a distal regulatory elements with a cas9-cas9 fusion for fetal hemoglobin re-induction. (PCT/WIPO)
(https://patents.google.com/patent/WO2019147302A1/en)
Programmable dna base editing by nme2cas9-deaminase fusion proteins ((PCT/WIPO))
(https://patents.google.com/patent/WO2020081568A1/)
Improved cas12a/nls mediated therapeutic gene editing platforms (PCT/WIPO)
(https://patents.google.com/patent/WO2021216674A1/en)
A cas9-pdbd base editor platform with improved targeting range and specificity (US Patent)
(https://www.freepatentsonline.com/y2023/0049455.html)
Prime editor system for in vivo genome editing (US Patent)
(https://patents.google.com/patent/US20230374476A1/en)