Dan Ye, Ph.D.

Education

• 9/2005 – 11/2008

Ph.D. at the Division of Biopharmaceutics, Leiden/Amsterdam Center for Drug Research, Leiden University, The Netherlands.

Research topics: ABC-transporters and lipid transfer proteins: important players in macrophage cholesterol homeostasis and atherosclerosis.

• 9/2002 – 6/2005

M.Sc. at the college of Life Sciences, Zhejiang University, Hangzhou, China. Major: Genetics.

• 9/1998 – 7/2002

B.Sc. at the college of Life Sciences, Zhejiang University, Hangzhou, China. Major: Biological technology.

Work experience

• 12/2014-present

Professor at the Molecular and Cell Biology (MCB) Research Lab, Institutes of Biomedical Sciences (IBS), Fudan University

Research topics: Acetylation regulation on metabolism; Epigenetic control by metabolites during tumorigenesis.

• 3/2011-12/2014

Associated professor at the Molecular and Cell Biology (MCB) Research Lab, Institutes of Biomedical Sciences (IBS), Fudan University

Research topics: Acetylation regulation on metabolism; Epigenetic control by metabolites during tumorigenesis.

• 9/2008 – 12/2010

Postdoctoral fellow at the Division of Biopharmaceutics, Leiden/Amsterdam Center for Drug Research, Leiden University, The Netherlands.

Research topics: The ABCs of Cardiovascular Disease: from the Pathogenesis of Atherosclerosis to Myocardial Ischemia.

Contact

Institutes of Biomedical Sciences, Fudan University, Shanghai 200032 Tel: +86 21 54237450

Email: yedan@fudan.edu.cn

Lab homepage: https://www.fudan-mcb.com

Biography

Dr. Dan Ye has been studying the metabolism-chromatin axis and the relevance of epigenetic and metabolic dysregulation in cancer development. Three representative achievements include: 1) Discovered several metabolic intermediateswhich regulate the activity of TET enzymes; 2) Discovered epigenetic enzymes are recruited by sequence-specific transcription factors to regulate target genes and cell metabolism; 3) Discovered the role of tumor-associated metabolites in malignant transformation and reshaping the TME. To date, a series of achievements were made including 44 SCI-indexed papers with over 3000 citations. Over the past 5 years, Dr. Ye published 13 research articles as (co)corresponding authors at Nat Cell Biol, Journal of Hepatology, ect.

Research Areas

How cells coordinate metabolic, epigenetic, and signaling pathways for survival and growth is a fundamental question of biological research. Increasing evidence suggests that the cellular transcriptional machinery and its chromatin-associated proteins integrate metabolic signals to mediate homeostatic or adaptive responses. Dr. Ye’s research group is involved in the crossing field of tumor metabolism and epigenetics.

Research interest

Current work is directed towards a better understanding the metabolism-chromatin axis and the relevance of epigenetic and metabolic dysregulation in a range of diseases including cancer. This may aid firm foundation for in-depth understanding of the mechanisms for epigenetic and metabolic dysregulation during tumorigenesis and identification of potential drug targets for treating cancer.

Selected Publications

1. Renqiang Sun, Zhiyong Zhang, Ruoxuan Bao, Xiaozhen Guo, Yuan Gu, Wenjing Yang, Jinsong Wei, Xinyu Chen, Lingfeng Tong, Jian Meng, Chen Zhong, Cheng Zhang, Jinye Zhang, Yiping Sun, Chen Ling, Xuemei Tong, Fa-Xing Yu, Hongxiu Yu, Weifeng Qu, Bing Zhao, Wei Guo, Maoxiang Qian, Hexige Saiyin, Ying Liu, Rong-Hua Liu, Cen Xie, Weiren Liu, Yue Xiong, Kun-Liang Guan, Yinghong Shi*, Pu Wang*, Dan Ye*. Loss of SIRT5 promotes bile acid-induced immunosuppressive microenvironment and hepatocarcinogenesis. J Hepatol. 2022;77(2):453-466.

2. Lei-Lei Chen#, Carmen Morcelle#, Zhou-Li Cheng#, Xiufei Chen, Yanping Xu, Yajing Gao, Junbin Song, Zhijun Li, Matthew D. Smith, Miao Shi, Yezhang Zhu, Neng Zhou, Meng Cheng, Chenxi He, Kwei-Yan Liu, Guoping Lu, Lei Zhang, Chen Zhang, Jingye Zhang, Yiping Sun, Tuan Qi, Yingying Lyu, Zhi-Zhong Ren, Xian-Ming Tan, Jiayong Yin, Fei Lan, Ying Liu, Hui Yang, Maoxiang Qian, Caiwen Duan, Xing Chang, Yufeng Zhou, Li Shen, Albert S. Baldwin, Kun-Liang Guan, Yue Xiong, and Dan Ye.* Itaconate Inhibits TET DNA Dioxygenases to Dampen Inflammatory Responses. Nat Cell Biol. 2022;24(3):353-363.

3. Xiufei Chen#, Wenjie Zhou#, Ren-Hua Song#, Shuang Liu#, Shu Wang, Yujia Chen, Chao Gao, Chenxi He, Jianxiong Xiao, Lei Zhang, Tianxiang Wang, Peng Liu, Kunlong Duan, Zhouli Cheng, Chen Zhang, Jinye Zhang, Yiping Sun, Felix Jackson, Fei Lan, Yun Liu, Yanhui Xu, Justin Jong-Leong Wong, Pu Wang, Hui Yang, Yue Xiong, Tong Chen*, Yan Li*, Dan Ye.* Tumor suppressor CEBPA interacts with and inhibits DNMT3A activity. Sci Adv. 2022;8(4):eabl5220

4. Cheng ZL, Zhang ML, Lin HP, Gao C, Song JB, Zheng Z, Li L, Zhang Y, Shen X, Zhang H, Huang Z, Zhan W, Zhang C, Hu X, Sun YP, Jiang L, Sun L, Xu Y, Yang C, Ge Y, Zhao Y, Liu X, Yang H, Liu P, Guo X, Guan KL, Xiong Y, Zhang M*, Ye D*.The Zscan4-Tet2 Transcription Nexus Regulates Metabolic Rewiring and Enhances Proteostasis to Promote Reprogramming. Cell Reports. 2020;32(2):107877.

5. Lei-Lei Chen#, Huai-Peng Lin#, Wen-Jie Zhou, Chen-Xi He, Zhi-Yong Zhang, Zhou-Li Cheng, Jun-Bin Song, Peng Liu, Xin-Yu Chen, Yu-Kun Xia, Xiu-Fei Chen, Ren-Qiang Sun, Jing-Ye Zhang, Yi-Ping Sun, Lei Song, Bing-Jie Liu, Rui-Kai Du, Chen Ding, Fei Lan, Sheng-Lin Huang, Feng-Zhou, Su-Ling Liu, Yue Xiong*, Dan Ye*, and Kun-Liang Guan*.SNIP1 recruits TET2 to regulate c-MYC target genes and cellular DNA damage response. Cell Reports. 2018;25(6):1485-1500.

6. D Ye*, KL Guan, Y Xiong*. Metabolism, Activity, and Targeting of D-and L-2-Hydroxyglutarates. Trends in Cancer. 2018;4(2):151-165 (Invited review)

7. Huai-Peng Lin, Zhou-Li Cheng, Ruo-Yu He, Lei Song, Meng-Xin Tian, Lisha Zhou, Beezly S. Groh, Weiren Liu, Min-Biao Ji, Chen Ding, Ying-Hong Shi, Kun-Liang Guan*, Dan Ye*, and Yue Xiong*. Destabilization of fatty acid synthase by acetylation inhibits de novo lipogenesis and tumor cell growth. Cancer Research. 2016;76, 6924-36

8. Ye D*, Xiong Y*. Cancer: Suffocation of gene expression. Nature. 2016;537(7618):42-43.

9. Wang P, Wu J, Ma S-H, Zhang L, Yao J, Hoadley KA, Wilkerson MD, Perou CM, Guan K-L*, Ye D*, Xiong Y. Oncometabolite D-2-Hydroxyglutarate Inhibits ALKBH DNA Repair Enzymes and Sensitizes IDH Mutant Cells to Alkylating Agents. Cell Reports. 2015;13(11):2353-61.

10. Wang S-W, Jiang B-W, Zhang T-F, Liu L-X, Wang Y, Wang Y-P, Chen X-F, Lin H-P, Zhou L-S, Xia Y-K, Chen L-L, Yang C, Xiong Y*, Ye D*, Guan K-L.* Insulin and mTOR Pathway Regulate HDAC3-Mediated Deacetylation and Activation of PGK1. PLoS Biology. 2015;13(9):e1002243 (Previewed by PLOS Biology)

11. Hui Yang#, Lisha Zhou#, Qian Shi, Yuzheng Zhao, Huaipeng Lin, Mengli Zhang, Yi Yang, Zhi-Qiang Ling, Kun-Liang Guan*, Yue Xiong*, and Dan Ye*. SIRT3-dependent GOT2 acetylation enhances the malate-aspartate NADH shuttle activity to promote pancreatic tumor growth. EMBO J. 2015;34(8):1110-25.

12. Wang Y-P, Xiao M-T, Chen X-F, Chen L-L, Xu Y-P, Lv L, Wang P, Yang H, Ma S-H, Lin H-P, Jiao B, Ren R-B, Ye D*, Guan, K-L*, and Xiong Y*. WT1 recruits TET2 to regulate its target gene expression and suppress leukemia cell proliferation. Mol Cell. 2015; 57(4):662-73 (Previewed by Mol Cell)

13. Wang YP, Zhou LS, Zhao YZ, Wang SW, Chen LL, Liu LX, Ling ZQ, Hu FJ, Sun YP, Zhang JY, Yang C, Yang Y, Xiong Y, Guan KL, Ye D*. Regulation of G6PD acetylation by KAT9/SIRT2 modulates NADPH homeostasis and cell survival during oxidative stress. EMBO J. 2014; 33(12):1304-20 (Previewed by EMBO J)

14. Yang H. Lin H-P, Xu H-Y, Zhang L, Cheng L, Wen B, Shou J-Y, Guan K-L, Xiong Y, Ye D*. TET-catalyzed 5-methylcytosine hydroxylation is dynamically regulated by metabolites. Cell Research. 2014;24(8):1017-20.

15. Yang H, Liu Y, Bai F, Zhang J-Y, Ma S-H, Liu J, Xu Z-D, Zhu H-G, Ling Z-Q, Ye D*, Guan K-L* and Xiong Y*. Tumor development is associated with decrease of TET gene expression and 5-methylcytosine hydroxylation. Oncogene. 2013; 32(5):663-9.

16. Ye D, Ma S-H, XiongY , GuanK-L*. R-2-Hydroxyglutarate as the Key Effector of IDH Mutations Promoting Oncogenesis. Cancer Cell. 2013; 23(3):274-276.

17. Ye D*, Guan K-L* and Xiong Y*. The mechanisms of IDH mutations in tumorigenesis. Cell Research. 2012; 22 (7):1102-4. (Invited review)

18. Xiao M, Yang H, Xu W, Ma S, Lin H, Zhu H, Liu L, Liu Y, Yang C, Xu Y, Zhao S, Ye D*, Xiong Y*, Guan KL. Inhibition of α-KG-dependent histone and DNA demethylases by fumarate and succinate that are accumulated in mutations of FH and SDH tumor suppressors. Genes & Development. 2012; 26(12):1326-1338.