PI, PhD

Institute of Metabolism and Integrative Biology, Fudan University

Email: chenli_imib@fudan.edu.cn

Office: Room 1308, Building D3, Bay Valley Science and Technology Park (Phase II), Yangpu District, Shanghai, China

Biography

Li Chen is a tenure-track associate professor at the Institute of Metabolism and Integrative Biology, Fudan University. He received his B.S. in Chemistry from Peking University in 2013 and his Ph.D. in Chemistry from Princeton University in 2019, followed by postdoctoral training at Princeton. He established his laboratory at Fudan in October 2020 and was appointed to his current position in February 2025.

His research focuses on metabolomics and metabolic regulation. His group develops methods to identify and quantify metabolites and applies these methods to study metabolic enzymes, transporters, and related metabolic processes. He has received funding as principal investigator from the National Natural Science Foundation of China (NSFC), including its Excellent Young Scientists Fund and General Program. He has also participated in research supported by the National Key R&D Program of China and the National Science and Technology Major Project.

He developed and teaches the graduate course “Designing Life Science Research Projects in the Age of AI” and contributes to other courses, including “Techniques and Methods in Metabolism Research.” He chairs the Youth Committee of the Metabolomics Division of the Biophysical Society of China and also serves as the division’s Deputy Secretary-General. At the institute, he leads the development and operation of mass spectrometry platforms for metabolomics, lipidomics, and metabolic flux analysis.

Research Interests

Our group uses mass spectrometry, computational approaches, and stable isotope tracing to study metabolites and their roles in biological processes. We focus on three areas:

1. Accurate metabolite identification. We develop metabolomics methods that use relationships among mass spectrometry signals and the chemical properties of compounds to improve metabolite identification and discover unknown metabolites.

2. Functions of metabolic enzymes and transporters. By measuring metabolite transport and changes in substrates and products, we investigate which metabolites transporters carry, which substrates enzymes act on, and how these activities are regulated.

3. Tracing metabolic pathways and fluxes. We use stable isotope tracing to determine where metabolites come from and how they move through metabolic pathways, examining how metabolism changes with nutrition and disease.

Selected Publications

# denotes co-first authorship; * denotes corresponding authorship.

1. Kaiwen Deng#, Ran Liu#, Ruiping He, Li Chen*. A Two-Layer Structural Key Framework for Linking Compound Identifiers and MS/MS Evidence in Spectral Database Curation. Metabolites. 2026, 16(7):435. doi: 10.3390/metabo16070435

2. Yuchen Huang#, Lexuan Hou#, Ruiping He#, Lin Zhu#, Caifeng Xu, Shixiang Duan, Jing Hu, Xi Yang, Yu-Hsuan Tsai, Chu Wang, Chunmao He*, Xiaoyu Li*, Li Chen*, Gang Li*. Scaling covalent ligand discovery through dynamic combinatorial library-versus-proteome screening. Nature Communications. 2026, 17:7753. doi: 10.1038/s41467-026-74672-y

3. Rui Lv#, Leiye Yu#, Jingyi Liu#, Youli Zhou#, Ruiping He#, Chen Wang, Bing Gan, Rujuan Ti, Haizhan Jiao, Baohui Song, Yiqi Chen, Feifei Lin, Mei Gao, Hongli Hu, Shankai Yin, Pinghong Zhou, Lizhe Zhu, Mingyan Cai, Tian Xie*, Jia Liu*, Li Chen*, Yunshi Zhong*, Ruobing Ren*. Molecular basis of HACD-TECR complex mediated very-long-chain fatty acid elongation reveal a potential target in colorectal cancer. Science Advances. 2026, 12(33):eaeh5593. doi: 10.1126/sciadv.aeh5593

4. Tong Sun#, Yizhu Tao#, Yingjie Zeng#, Ran Ai#, Tong Li, Xinyu Li, Xueshan Li, Ruiping He, Zhikun Jia, Xiaohan Sun, Zhuanghui Feng, Xiangyi Liu, Xingyu Kong, Linzhang Huang, Lei Chen, Jinfei Ni*, Li Chen*, Wei Dai*. Increased yolk lipid mobilization promotes zebrafish post-segmentation growth via an Hnf4-lipoprotein axis. Cell Reports. 2026, 45(5):117295. doi: 10.1016/j.celrep.2026.117295

5. Liucheng Li#, Jianwei You#, Zi-Qing Chai#, Xueshan Li, Xinlei Cai, Lin Wang, Fang Yang, Lingzhi Zhu, Wen Mi, Xinyi Xia, Haohang Yan, Fei Li, Juan Wang, Tong-Jin Zhao, Ligong Chen, Hongbin Ji, Pingyu Liu, Xiao-Long Zhou*, Li Chen*, Fuming Li*. SLC6A6 imports taurine into mitochondria to sustain mitochondrial translation and tumour growth. Nature Metabolism. 2026, 8:704–721. doi: 10.1038/s42255-026-01455-6

6. Jing Feng#, Xueshan Li#, Xin Teng#, Dingding Fan#, Jin Yin, Yanci Qiu, Ziling Yi, Li Chen*, Haoqian M. Zhang*, Chitong Rao*. Harnessing CO2 fixation and reducing power recycling for enhanced polyhydroxyalkanoates industrial bioproduction. Metabolic Engineering. 2025, 91:204–216. doi: 10.1016/j.ymben.2025.04.009

7. Xiaowen Zhang#, Ang Jia#, Jianwei You#, Zixuan Zhuang, Yinfei Wang, Ting Liu, Xingrong Du, Linzhang Huang, Peng Li, Tong-Jin Zhao, Craig T. Jordan, Li Chen*, Ji-Hao Zhou*, Haobin Ye*. Purine metabolites regulate leukemic cell sensitivity toward cytarabine. Haematologica. 2025, 110(5):1170–1176. doi: 10.3324/haematol.2024.286308

8. Bin Pang#, Leiye Yu#, Tong Li#, Haizhan Jiao, Xiaomei Wu, Jinxin Wang, Ruiping He, Yurou Zhang, Juan Wang, Hongli Hu, Wei Dai*, Li Chen*, Ruobing Ren*. Molecular basis of Spns2-facilitated sphingosine-1-phosphate transport. Cell Research. 2024, 34(2):173–176. doi: 10.1038/s41422-023-00908-x

9. Kun-Long Duan#, Tian-Xiang Wang#, Jian-Wei You#, Hai-Ning Wang, Zhi-Qiang Wang, Zi-Xuan Huang, Jin-Ye Zhang, Yi-Ping Sun, Yue Xiong, Kun-Liang Guan, Dan Ye, Li Chen*, Ronghua Liu*, Hai-Xin Yuan*. PCK2 maintains intestinal homeostasis and prevents colitis by protecting antibody-secreting cells from oxidative stress. Immunology. 2024, 173(2):339–359. doi: 10.1111/imm.13827

10. Zhikun Jia, Qiongju Qiu, Ruiping He, Tianyu Zhou, Li Chen*. Identification of metabolite interference is necessary for accurate LC-MS targeted metabolomics analysis. Analytical Chemistry. 2023, 95(20):7985–7992. doi: 10.1021/acs.analchem.3c00804

11. Xiaomei Wu#, Bin Pang#, Jianwei You, Leiye Yu, Ruobing Ren*, Hongyang Wang*, Li Chen*. An LC-MS-based workflow measures the export activity of S1P transporters. Biochemical and Biophysical Research Communications. 2023, 668:118–124. doi: 10.1016/j.bbrc.2023.05.014

12. Mingyu Fang#, Xing Wang#, Zhikun Jia, Qiongju Qiu, Peng Li, Li Chen*, Hui Yang*. A simple and efficient method for the substrate identification of amino acid decarboxylases. International Journal of Molecular Sciences. 2022, 23(23):14551. doi: 10.3390/ijms232314551

13. Li Chen, Wenyun Lu, Lin Wang, Xi Xing, Ziyang Chen, Xin Teng, Xianfeng Zeng, Antonio D. Muscarella, Yihui Shen, Alexis Cowan, Melanie R. McReynolds, Brandon J. Kennedy, Ashley M. Lato, Shawn R. Campagna, Mona Singh, Joshua D. Rabinowitz*. Metabolite discovery through global annotation of untargeted metabolomics data. Nature Methods. 2021, 18(11):1377–1385. doi: 10.1038/s41592-021-01303-3

14. Li Chen, Zhaoyue Zhang, Atsushi Hoshino, Henry D. Zheng, Michael Morley, Zoltan Arany, Joshua D. Rabinowitz*. NADPH production by the oxidative pentose phosphate pathway supports folate metabolism. Nature Metabolism. 2019, 1:404–415. doi: 10.1038/s42255-019-0043-x

15. Michael A. Estrella#, Jin Du#, Li Chen#, Sneha Rath, Eliza Prangley, Alisha Chitrakar, Tsutomu Aoki, Paul Schedl, Joshua D. Rabinowitz*, Alexei Korennykh*. The metabolites NADP+ and NADPH are targets of the circadian protein Nocturnin. Nature Communications. 2019, 10:2367. doi: 10.1038/s41467-019-10125-z

16. Zhaoyue Zhang#, Li Chen#, Ling Liu, Xiaoyang Su*, Joshua D. Rabinowitz*. Chemical Basis for Deuterium Labeling of Fat and NADPH. Journal of the American Chemical Society. 2017, 139:14368–14371. doi: 10.1021/jacs.7b08012

17. Li Chen, Gregory S. Ducker, Wenyun Lu, Xin Teng, Joshua D. Rabinowitz*. An LC-MS chemical derivatization method for the measurement of five different one-carbon states of cellular tetrahydrofolate. Analytical and Bioanalytical Chemistry. 2017, 409:5955–5964. doi: 10.1007/s00216-017-0514-4

Other Publications

1. Hantao Qiang#, Fei Wang#, Wenyun Lu, Xi Xing, Hahn Kim, Sandrine A. M. Mérette, Lucas B. Ayres, Eponine Oler, Jenna E. AbuSalim, Asael Roichman, Michael Neinast, Ricardo A. Cordova, Won Dong Lee, Ehud Herbst, Vishu Gupta, Samuel L. Neff, Mickel Hiebert-Giesbrecht, Adamo Young, Vasuk Gautam, Siyang Tian, Bo Wang, Hannes Röst, Jatinder Baidwan, Russell Greiner, Li Chen, Chad W. Johnston, Leonard J. Foster, Aaron M. Shapiro, David S. Wishart, Joshua D. Rabinowitz, Michael A. Skinnider*. Language model-guided anticipation and discovery of mammalian metabolites. Nature. 2026, 651(8104):211–220. doi: 10.1038/s41586-025-09969-x

2. Lingzhi Zhu, Kuishen Wu, Jianwei You, Wen Mi, Jie Xu, Liucheng Li, Fang Yang, Xinyi Xia, Haohang Yan, Fei Li, Li Chen, Pingyu Liu, Fuming Li*. Mitochondrial glutamine import sustains electron transport chain integrity independently of glutaminolysis in cancer. Molecular Cell. 2026, 86(1):151–165.e9. doi: 10.1016/j.molcel.2025.12.001

3. Yaxin Niu#, Shengmin Hu#, Yanfeng Zhang, Jinbao Yang, Jiarui Zhang, Ruiping He, Li Chen, Lin Xu, Hongfang Zhao, Bing Gan, Ruobing Ren, Ruth J. F. Loos, Haobin Ye, Xingrong Du, Tongjin Zhao, Peng Li, Antonio Vidal-Puig, Linzhang Huang*. Lactate-activated GPR81/FARP1 signaling drives insulin-independent glucose uptake and metabolic control. Cell Research. 2026, 36(2):137–151. doi: 10.1038/s41422-025-01207-3

4. Li Yang, Jianwei You, Xincheng Yang, Ruishu Jiao, Jie Xu, Yue Zhang, Wen Mi, Lingzhi Zhu, Youqiong Ye, Ruobing Ren, Delin Min, Meilin Tang, Li Chen, Fuming Li, Pingyu Liu*. ACSS2 drives senescence-associated secretory phenotype by limiting purine biosynthesis through PAICS acetylation. Nature Communications. 2025, 16(1):2071. doi: 10.1038/s41467-025-57334-3

5. Li Weng#, Wen-Shuai Tang#, Xu Wang#, Yingyun Gong#, Changqin Liu, Ni-Na Hong, Ying Tao, Kuang-Zheng Li, Shu-Ning Liu, Wanzi Jiang, Ying Li, Ke Yao, Li Chen, He Huang, Yu-Zheng Zhao, Ze-Ping Hu, Youli Lu, Haobin Ye, Xingrong Du, Hongwen Zhou*, Peng Li*, Tong-Jin Zhao*. Surplus fatty acid synthesis increases oxidative stress in adipocytes and induces lipodystrophy. Nature Communications. 2024, 15(1):133. doi: 10.1038/s41467-023-44393-7

6. Xinlu Han#, Deyu Wang#, Liao Yang, Ning Wang, Jianliang Shen, Jinghan Wang, Lei Zhang, Li Chen, Shenglan Gao, Wei-Xing Zong*, Yongbo Wang*. Activation of polyamine catabolism promotes glutamine metabolism and creates a targetable vulnerability in lung cancer. Proceedings of the National Academy of Sciences. 2024, 121(13):e2319429121. doi: 10.1073/pnas.2319429121

7. Wen Mi, Jianwei You, Liucheng Li, Lingzhi Zhu, Xinyi Xia, Li Yang, Fei Li, Yi Xu, Junfeng Bi, Pingyu Liu, Li Chen, Fuming Li*. BET inhibition induces GDH1-dependent glutamine metabolic remodeling and vulnerability in liver cancer. Life Metabolism. 2024, 3(4):loae016. doi: 10.1093/lifemeta/loae016

8. Bruce Culbertson#, Kristle Garcia#, Daniel Markett, Hosseinali Asgharian, Li Chen, Lisa Fish, Albertas Navickas, Johnny Yu, Brian Woo, Arjun Scott Nanda, Benedict Choi, Shaopu Zhou, Joshua Rabinowitz, Hani Goodarzi*. A sense-antisense RNA interaction promotes breast cancer metastasis via regulation of NQO1 expression. Nature Cancer. 2023, 4(5):682–698. doi: 10.1038/s43018-023-00554-7

9. Tianxia Xiao, Artem Khan, Yihui Shen, Li Chen, Joshua D. Rabinowitz*. Glucose feeds the tricarboxylic acid cycle via excreted ethanol in fermenting yeast. Nature Chemical Biology. 2022, 18(12):1380–1387. doi: 10.1038/s41589-022-01091-7

10. Melanie R. McReynolds#, Karthikeyani Chellappa#, Eric Chiles, Connor Jankowski, Yihui Shen, Li Chen, Hélène C. Descamps, Sarmistha Mukherjee, Yashaswini R. Bhat, Siddharth R. Lingala, Qingwei Chu, Paul Botolin, Faisal Hayat, Tomohito Doke, Katalin Susztak, Christoph A. Thaiss, Wenyun Lu, Marie E. Migaud, Xiaoyang Su, Joshua D. Rabinowitz*, Joseph A. Baur*. NAD+ flux is maintained in aged mice despite lower tissue concentrations. Cell Systems. 2021, 12(12):1160–1172.e4. doi: 10.1016/j.cels.2021.09.001

11. Cholsoon Jang, Li Chen, Joshua D. Rabinowitz*. Metabolomics and Isotope Tracing. Cell. 2018, 173(4):822–837. doi: 10.1016/j.cell.2018.03.055