Including learning experience
PhD in Pathogen Biology (2000-2003), China Centre of Disease Control and Prevention, Beijing, China
MS in Biochemistry and Molecular Biology (1997-2000), Wuhan Institute of Virology, Chinese Academy of Science, Wuhan, China
BS in Biology (1991-1995), School of Biology, University of Hubei, Wuhan, China

 

Work Experience
Associate Professor and Professor (2010 – Present), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
Research Associate (2008 – 2010), Cambridge Institute of Medical Research, University of Cambridge, Cambridge, UK.
Postdoctoral Fellow (2003-2008), Genome Institute of Singapore, Singapore

 

 

Social Service
Member of Human Genome Organisation (HUGO)

We focus on the developing various deep-sequencing based approaches to understand the transcription factor-mediated transcriptional network and epigenomic regulation in both stem cells and cancer cells. Our research work includes：1）epignomic modifications in stem cells and their effect on cell fate decision;；2）alternative polyadenylation and this implication in tumorigenesis；3）development and application of epigenomic profiling approaches for small cell numbers or single cells. We have authored more than 30 papers in Cell Stem Cell, Cell, Nature, PNAS, Genome Biology and J Exp Clin Cancer Res with the citation of more than 5600.

1. Hu C, Wu J, Li P, Zhang Y, Peng Y, Liu R, Du W, Kang Y, Sun J, Wu J, Shao Z, Zhao X. 2cChIP-seq and 2cMeDIP-seq: The Carrier-Assisted Methods for Epigenomic Profiling of Small Cell Numbers or Single Cells. Int J Mol Sci. 2022; 23(22):13984.
2. Tan S, Zhang M, Shi X, Ding K, Zhao Q, Guo Q, Wang H, Wu Z, Kang Y, Zhu T, Sun J, Zhao X. CPSF6 links alternative polyadenylation to metabolism adaption in hepatocellular carcinoma progression. J Exp Clin Cancer Res. 2021;40(1):85.
3. Song W, Shi X, Xia Q, Yuan M, Liu J, Hao K, Qian Y, Zhao X, Zou K. PLZF suppresses differentiation of mouse spermatogonial progenitor cells via binding of differentiation associated genes. J Cell Physiol. 2020;235(3):3033-3042.
4. Zhao Q, Shi X, Chen Y, Bi L, Tian J, Zhang M, Xu L, Sun J, Zhao X. Transcriptome-wide alternative polyadenylation profiling reveals the herbal formula Yangyinjiedu-induced preferential poly(A) usage in lung adenocarcinoma cells. Acta Biochim Biophys Sin (Shanghai). 2020;52(10):1171-1174.
5. Kang Y, Ooi HS, Zhao X. Transcript Profiling Analysis Through Paired-End Ditag (PET) Approach Coupled with Deep Sequencing Reveals Transcriptome Complexity in Yeast. Methods Mol Biol. 2019;2049:105-112.
6. Yang W, Kang Y, Zhao Q, Bi L, Jiao L, Gu Y, Lu J, Yao J, Zhou D, Sun J, Zhao X, Xu L. Herbal formula Yangyinjiedu induces lung cancer cell apoptosis via activation of early growth response 1. J Cell Mol Med. 2019 Sep;23(9):6193-6202.
7. Gu Y, Wu J, Yang W, Xia C, Shi X, Li H, Sun J, Shao Z, Wu J, Zhao X. STAT3 is required for proliferation and exhibits cell type-specific binding preference in mouse female germline stem cells. Mol. Omics, 2018;14(2):95-102.
8. Tan S, Li H, Zhang W, Shao Y, Liu Y, Guan H, Wu J, Zhu Y, Cai H, Chen C, Lobie PE, Zhao X, Sun J, Zhu T. NUDT21 Negatively Regulates PSMB2 and CXXC5 by Alternative Polyadenylation and Contributes to Hepatocellular Carcinoma Suppression. Oncogene. 2018;37(35):4887-4900.
9. Wu J, Xiao Y, Xia C, Yang F, Li H, Shao Z, Lin Z, Zhao X. Identification of Biomarkers for Predicting Lymph Node Metastasis of Stomach Cancer Using Clinical DNA Methylation Data. Dis Markers. 2017; 2017:5745724.
10. Zhang XL, Wu J, Wang J, Shen T, Li H, Lu J, Gu Y, Kang Y, Wong CH, Ngan CY, Shao Z, Wu J, Zhao X. Integrative epigenomic analysis reveals unique epigenetic signatures involved in unipotency of mouse female germline stem cells. Genome Biol. 2016;17(1):162.
11. Lu J, Chen J, Xu N, Wu J, Kang Y, Shen T, Kong H, Ma C, Cheng M, Shao Z, Xu L, Zhao X. Activation of AIFM2 enhances apoptosis of human lung cancer cells undergoing toxicological stress. Toxicol Lett. 2016;258:227-36.
12. Lai DP, Tan S, Kang YN, Wu J, Ooi HS, Chen J, Shen TT, Qi Y, Zhang X, Guo Y, Zhu T, Liu B, Shao Z, Zhao X. Genome-wide profiling of polyadenylation sites reveals a link between selective polyadenylation and cancer metastasis. Hum Mol Genet. 2015; 24(12): 3410-7.
13. Li H, Hou J, Bai L, Hu C, Tong P, Kang Y, Zhao X, Shao Z. Genome-wide Analysis of Core Promoter Structures in Schizosaccharomyces pombe with DeepCAGE. RNA Biol. 2015; 12(5): 525--537.
14. Qi Y, Zhang X, Kang Y, Wu J, Chen J, Li H, Guo Y, Liu B, Shao Z, Zhao X. Genome-wide transcriptional profiling analysis reveals annexin A6 as a novel EZH2 target gene involving gastric cellular proliferation. Mol Biosyst. 2015; 11(7):1925-32.
15. Zhao X, Han X, Chew JL, Liu J, Chiu KP, Choo A, Orlov YL, Sung WK, Shahab A, Kuznetsov VA, Bourque G, Oh S, Ruan Y, Ng HH, Wei CL. Whole genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells. Cell Stem Cell, 2007; 1 (3):286-9.
16. ENCODE Project Consortium (including Zhao X). Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007; 447(7146):799-816.
17. Wei CL, Wu Q, Vega VB, Chiu KP, Ng P, Zhang T, Shahab A, Yong HC, Fu Y, Weng Z, Liu J, Zhao X, Chew JL, Lee YL, Kuznetsov VA, Sung WK, Miller LD, Lim B, Liu ET, Yu Q, Ng HH, Ruan Y. A global map of p53 ranscription- factor binding sites in the human genome. Cell. 2006; 124(1):207-19.

1. Characterization of NUDT21-induced alteration in poly(A) sites and its tumor suppressor function in hepatocellular carcinoma cells. National Natural Science Fundation, grant no. 31671299 (2016.1-2020.12), PI.
2. Characterization of the regulation mechanisms for mammalian spermatogenesis. National Key Research and Development Program of China, grant no. 2018YFC1003501, team member.
3. The clinical observation and the related metastatic mechanism investigation of Feiyanning-treated non-small cell lung cancer cell patients at stage Ib-IIIa. Interdisciplinary Program of Shanghai Jiao Tong University, grant No.
270 YG2019ZDA25 (2020.1-2022.12)，co-PI.
4. Mechanism investigation of germ line stem cells and germ cells transformed from spermatogonia. 973 program of China, grant no. 2013CB967402，team member。
5. Characterization of transcriptional regulation network in gastric MALT lymphoma. National Natural Science Fundation, grant no. 91229123 (2013.1-2015.12), PI.
6. The transcriptional regulation network-based characterization of mechanism of traditional Chinese medicine, project of traditional Chinese medicine clinical study base of National administration of traditional Chinese medicine, grant no. JDZX2012123 (2013.1-2015.12), PI.
7. Characterization of genome-wide H3K4me3 and H3K27me3 modifications in mouse female germline stem cells.National Natural Science Fundation, grant no. 91010004 (2011.1-2013.12)，PI.

PhD student：4
Master student：2