Principal investigator
Name:
Xue-Song LiuAssociate Professor , PhD, Associate Professor
Position:
Affiliation:
School of Life Science and Technology
Honor:
Education Background:
- 1998/09-2002/07, Wuhan University, B.S.
- 2002/09-2007/07, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Ph.D.
Working Experience:
- 2008/10-2015/05, Medical School and School of Public Health of Harvard University, Postdoctoral Fellow
- 2015/06-2022/09, School of Life Science and Technology, ShanghaiTech University, Assistant Professor (TENURE-TRACK)
- 2022/09-Now, School of Life Science and Technology, ShanghaiTech University, Associate Professor (TENURED)
Group Introduction
Research Area:
Cancer Biology
Research Interests:
Cancers are majorly caused by mutations or aberrant expression of cancer genes. We are interested in the molecular and genetic study of human cancer, and will use multiple approaches, including biochemistry, cell biology, bioinformatics and mouse model to study the genomics of human cancer. We will identify and study the function of novel cancer genes, particularly those genes that play roles in regulating chromatin structure and RNA biogenesis. We are also interested in therapeutically targeting cancer cells with defined common genetic alterations.
Representative Publications (*First Author, # Corresponding Author)
- 1. Ning, Wei*; Wu, Tao; Wu, Chenxu; Wang, Shixiang; Tao, Ziyu; Wang, Guangshuai; Zhao, Xiangyu; Diao, Kaixuan; Wang, Jinyu; Chen, Jing; Chen, Fuxiang; Liu, Xue-Song#.Accurate prediction of pan-cancer types using machine learning with minimal number of DNA methylation sites.JOURNAL OF MOLECULAR CELL BIOLOGY. Apr 2023.
- 2. Wang, Guangshuai*; Wu, Tao; Ning, Wei; Diao, Kaixuan; Sun, Xiaoqin; Wang, Jinyu; Wu, Chenxu; Chen, Jing; Xu, Dongliang; Liu, Xue-Song#.TLimmuno2: predicting MHC class II antigen immunogenicity through transfer learning.BRIEFINGS IN BIOINFORMATICS. Mar 2023.
- 3. Tao, Ziyu*; Wang, Shixiang; Wu, Chenxu; Wu, Tao; Zhao, Xiangyu; Ning, Wei; Wang, Guangshuai; Wang, Jinyu; Chen, Jing; Diao, Kaixuan; Chen, Fuxiang; Liu, Xue-Song#.The repertoire of copy number alteration signatures in human cancer.BRIEFINGS IN BIOINFORMATICS. 01 Feb 2023.
- 4. Wu, Tao*; Diao, Kaixuan; Liu, Xue-Song#.Quantification of Neoantigen-Mediated Immunoediting in Cancer Evolution-Reply.CANCER RESEARCH. Mar 2023. 83(6):973.
- 5. Diao, Kaixuan*; Chen, Jing; Wu, Tao; Wang, Xuan; Wang, Guangshuai; Sun, Xiaoqin; Zhao, Xiangyu; Wu, Chenxu; Wang, Jinyu; Yao, Huizi; Gerarduzzi, Casimiro; Liu, Xue-Song#.Seq2Neo: A Comprehensive Pipeline for Cancer Neoantigen Immunogenicity Prediction.INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES. Oct 2022. 23(19).
- 6. Zhao, Xiangyu*; Chen, Yuxing; Sun, Xiaoqin; He, Zaoke; Wu, Tao; Wu, Chenxu; Chen, Jing; Wang, Jinyu; Diao, Kaixuan; Liu, Xue-Song#.Oncogenic EFNA4 Amplification Promotes Lung Adenocarcinoma Lymph Node Metastasis.CANCERS. Sep 2022. 14(17).
- 7. Jianfeng Li#*; Benben Miao*; Shixiang Wang*; Wei Dong*; Houshi Xu*; Chenchen Si*; Wei Wang; Songqi Duan; Jiacheng Lou; Zhiwei Bao; Hailuan Zeng; Zengzeng Yang; Wenyan Cheng; Fei Zhao; Jianming Zeng; Xue-Song Liu#; Renxie Wu#; Yang Shen#; Zhu Chen#; Saijuan Chen#; Mingjie Wang#.Hiplot: a comprehensive and easy-to-use web service for boosting publication-ready biomedical data visualization.BRIEFINGS IN BIOINFORMATICS. Jul 2022.
- 8. Wu, Tao*; Wang, Guangshuai; Wang, Xuan; Wang, Shixiang; Zhao, Xiangyu; Wu, Chenxu; Ning, Wei; Tao, Ziyu; Chen, Fuxiang; Liu, Xue-Song#.Quantification of neoantigen-mediated immunoediting in cancer evolution.CANCER RESEARCH. 15 Jun 2022. 82(12).
- 9. Wu, Tao*; Wu, Chenxu*; Zhao, Xiangyu; Wang, Guangshuai; Ning, Wei; Tao, Ziyu; Chen, Fuxiang; Liu, Xue-Song#.Extrachromosomal DNA formation enables tumor immune escape potentially through regulating antigen presentation gene expression.SCIENTIFIC REPORTS. Mar 2022.
- 10. He, Zaoke*; Sun, Xiaoqin; Wang, Shixiang; Bai, Dongsheng; Zhao, Xiangyu; Han, Ying; Hao, Piliang; Liu, Xue-Song#.Ggct (g-glutamyl cyclotransferase) plays an important role in erythrocyte antioxidant defense and red blood cell survival.BRITISH JOURNAL OF HAEMATOLOGY. Oct 2021. 195(2):267-275.
- 11. Wang, Shixiang*; Xiong, Yi; Zhao, Longfei; Gu, Kai; Li, Yin; Zhao, Fei; Li, Jianfeng; Wang, Mingjie; Wang, Haitao; Tao, Ziyu; Wu, Tao; Zheng, Yichao; Li, Xuejun#; Liu, Xue-Song#.UCSCXenaShiny: An R/CRAN Package for Interactive Analysis of UCSC Xena Data.BIOINFORMATICS. Jul 2021. 38(2).
- 12. Wang, Shixiang*; Li, Huimin; Song, Minfang; Tao, Ziyu; Wu, Tao; He, Zaoke; Zhao, Xiangyu; Wu, Kai; Liu, Xue-Song#.Copy number signature analysis tool and its application in prostate cancer reveals distinct mutational processes and clinical outcomes.PLOS GENETICS. May 2021.
- 13. He, Zaoke*; Wu, Tao; Wang, Shixiang; Zhang, Jing; Sun, Xiaoqin; Tao, Ziyu; Zhao, Xiangyu; Li, Huimin; Wu, Kai; Liu, Xue-Song#.Pan-cancer noncoding genomic analysis identifies functional CDC20 promoter mutation hotspots.ISCIENCE. Mar 2021.
- 14. Wang, Shixiang*; Tao, Ziyu; Wu, Tao; Liu, Xue-Song#.Sigflow: an automated and comprehensive pipeline for cancer genome mutational signature analysis.BIOINFORMATICS. 01 Jun 2021.
- 15. Wang, Shixiang*; He, Zaoke; Wang, Xuan; Li, Huimin; Liu, Xue-Song#.Antigen presentation and tumor immunogenicity in cancer immunotherapy response prediction.ELIFE. 26 Nov 2019. 8.
- 16. Wang, Shixiang*; Jia, Mingming*; He, Zaoke; Liu, Xue-Song#.APOBEC3B and APOBEC mutational signature as potential predictive markers for immunotherapy response in non-small cell lung cancer.ONCOGENE. 19 Jul 2018. 37(29):3924-3936.
- 17. Wang, Shixiang*; Zhang, Jing; He, Zaoke; Wu, Kai; Liu, Xue-Song#.The predictive power of tumor mutational burden in lung cancer immunotherapy response is influenced by patients' sex.INTERNATIONAL JOURNAL OF CANCER. 15 Nov 2019. 145(10):2840-2849.
- 18. He, Zaoke*; Wang, Shixiang; Shao, Yuanyuan; Zhang, Jing; Wu, Xiaolin; Chen, Yuxing; Hu, Junhao; Zhang, Feng; Liu, Xue-Song#.Ras Downstream Effector GGCT Alleviates Oncogenic Stress.ISCIENCE. 27 Sep 2019. 19:256-266.
- 19. Wang, Shixiang*; Cowley, Li An*; Liu, Xue-Song#.Sex Differences in Cancer Immunotherapy Efficacy, Biomarkers, and Therapeutic Strategy.MOLECULES. Sep 2019. 24(18).
- 20. Shixiang Wang*; Xuesong Liu#.The UCSCXenaTools R package: a toolkit for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq.JOURNAL OF OPEN SOURCE SOFTWARE. 05 Aug 2019. 4(40).
- 21. Wang, Shixiang*; He, Zaoke; Wang, Xuan; Li, Huimin; Wu, Tao; Sun, Xiaoqin; Wu, Kai; Liu, Xue-Song#.Can tumor mutational burden determine the most effective treatment for lung cancer patients?.LUNG CANCER MANAGEMENT. Dec 2019. 8(4).
- 22. Chen, Ming*; Zhang, Jiangwen; Sampieri, Katia; Clohessy, John G.; Mendez, Lourdes; Gonzalez-Billalabeitia, Enrique; Liu, Xue-Song; Lee, Yu-Ru; Fung, Jacqueline; Katon, Jesse M.; Menon, Archita Venugopal; Webster, Kaitlyn A.; Ng, Christopher; Palumbieri, Maria Dilia; Diolombi, Moussa S.; Breitkopf, Susanne B.; Teruya-Feldstein, Julie; Signoretti, Sabina; Bronson, Roderick T.; Asara, John M.; Castillo-Martin, Mireia; Cordon-Cardo, Carlos; Pandolfi, Pier Paolo#.An aberrant SREBP-dependent lipogenic program promotes metastatic prostate cancer.NATURE GENETICS. 2018. 50(2):206+.
- 23. Gerarduzzi, Casimiro*; de Polo, Anna; Liu, Xue-Song; El Kharbili, Manale; Little, John B.; Yuan, Zhi-Min#.Human epidermal growth factor receptor 4 (Her4) Suppresses p53 Protein via Targeting the MDMX-MDM2 Protein Complex IMPLICATION OF A NOVEL MDMX SER-314 PHOSPHOSITE.JOURNAL OF BIOLOGICAL CHEMISTRY. 2016. 291(50):25937-25949.
- 24. Liu, X-S*; Liu, Z.; Gerarduzzi, C.; Choi, D. E.; Ganapathy, S.; Pandolfi, P. P.; Yuan, Z-M#.Somatic human ZBTB7A zinc finger mutations promote cancer progression.ONCOGENE. 09 Jun 2016. 35(23):3071-3078.
- 25. Liu, Xue-Song*; Chandramouly, Gurushankar; Rass, Emilie; Guan, Yinghua; Wang, Guocan; Hobbs, Robin M.; Rajendran, Anbazhagan; Xie, Anyong; Shah, Jagesh V.; Davis, Anthony J.; Scully, Ralph#; Lunardi, Andrea#*; Pandolfi, Pier Paolo#.LRF maintains genome integrity by regulating the non-homologous end joining pathway of DNA repair.NATURE COMMUNICATIONS. 2015. 6.
- 26. Liu, Xue-Song*; Genet, Matthew D.; Haines, Jenna E.; Mehanna, Elie K.; Wu, Shaowei; Chen, Hung-I Harry; Chen, Yidong; Qureshi, Abrar A.; Han, Jiali; Chen, Xiang; Fisher, David E.; Pandolfi, Pier Paolo; Yuan, Zhi-Min#.ZBTB7A Suppresses Melanoma Metastasis by Transcriptionally Repressing MCAM.MOLECULAR CANCER RESEARCH. 2015. 13(8):1206-1217.
- 27. Liu, Xue-Song*; Little, John B.; Yuan, Zhi-Min#.Glycolytic metabolism influences global chromatin structure.ONCOTARGET. 2015. 6(6):4214-4225.
- 28. Gonzalez-Billalabeitia, Enrique*; Seitzer, Nina; Song, Su Jung; Song, Min Sup; Patnaik, Akash; Liu, Xue-Song; Epping, Mirjam T.; Papa, Antonella; Hobbs, Robin M.; Chen, Ming; Lunardi, Andrea; Ng, Christopher; Webster, Kaitlyn A.; Signoretti, Sabina; Loda, Massimo; Asara, John M.; Nardella, Caterina; Clohessy, John G.; Cantley, Lewis C.; Pandolfi, Pier Paolo#.Vulnerabilities of PTEN-TP53-Deficient Prostate Cancers to Compound PARP-PI3K Inhibition.CANCER DISCOVERY. 2014. 4(8):896-904.
- 29. Liu, Xue-Song*; Haines, Jenna E.; Mehanna, Elie K.; Genet, Matthew D.; Ben-Sahra, Issam; Asara, John M.; Manning, Brendan D.; Yuan, Zhi-Min#.ZBTB7A acts as a tumor suppressor through the transcriptional repression of glycolysis.GENES & DEVELOPMENT. 2014. 28(17):1917-1928.
- 30. Wang, Guocan*; Lunardi, Andrea; Zhang, Jiangwen; Chen, Zhenbang; Ala, Ugo; Webster, Kaitlyn A.; Tay, Yvonne; Gonzalez-Billalabeitia, Enrique; Egia, Ainara; Shaffer, David R.; Carver, Brett; Liu, Xue-Song; Taulli, Riccardo; Kuo, Winston Patrick; Nardella, Caterina; Signoretti, Sabina; Cordon-Cardo, Carlos; Gerald, William L.; Pandolfi, Pier Paolo#.Zbtb7a suppresses prostate cancer through repression of a Sox9-dependent pathway for cellular senescence bypass and tumor invasion.NATURE GENETICS. 2013. 45(7):739+.
- 31. Zhang, Hong-Xin*; Liu, Zi-Xing; Sun, Yue-Ping; Zhu, Jiang; Lu, Shun-Yuan; Liu, Xue-Song; Huang, Qiu-Hua; Xie, Yin-Yin; Zhu, Hou-Bao; Dang, Su-Ying; Chen, Hai-Feng; Zheng, Guang-Yong; Li, Yi-Xue; Kuang, Ying; Fei, Jian; Chen, Sai-Juan; Chen, Zhu#; Wang, Zhu-Gang#.Rig-I regulates NF-kappa B activity through binding to Nf-kappa b1 3 '-UTR mRNA.PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2013. 110(16):6459-6464.
- 32. Xue-Song Liu*; Xu-Dong Zhao*; Xiaoxing Wang*; Yi-Xin Yao; Liang-Liang Zhang; Run-Zhe Shu; Wei-Hua Ren; Ying Huang; Lei Huang; Ming-Min Gu; Ying Kuang; Long Wang; Shun-Yuan Lu; Jun Chi; Jing-Sheng Fen; Yi-Fei Wang; Jian Fei; Wei Dai#; Zhu-Gang Wang#.Germinal Cell Aplasia in Kif18a Mutant Male Mice Due to Impaired Chromosome Congression and Dysregulated BubR1 and CENP-E.GENES CANCER. Jan 2010. 1(1):26-39.
- 33. Shu, Run-Zhe#*; Zhang, Feng; Liu, Xue-Song; Li, Chun-Liang; Wang, Long; Tai, Yi-Lin; Wu, Xiao-Lin; Yang, Xue; Liao, Xiao-Dong; Jin, Ying; Gu, Ming-Min; Huang, Lei; Pang, Xiao-Fen#; Wang, Zhu-Gang#.Target Deletion of the Cytoskeleton-Associated Protein Palladin Does Not Impair Neurite Outgrowth in Mice.PLOS ONE. 2009. 4(9).
- 34. Wu, Xiao-lin*; Gu, Ming-min; Huang, Lei; Liu, Xue-song; Zhang, Hong-xin; Ding, Xiao-yi; Xu, Jian-qing; Cui, Bin; Wang, Long; Lu, Shun-yuan; Chen, Xiao-yi; Zhang, Hai-guo; Huang, Wei; Yuan, Wen-tao; Yang, Jiang-ming; Gu, Qun; Fei, Jian; Chen, Zhu; Yuan, Zhi-min; Wang, Zhu-gang#.Multiple Synostoses Syndrome Is Due to a Missense Mutation in Exon 2 of FGF9 Gene.AMERICAN JOURNAL OF HUMAN GENETICS. 2009. 85(1):53-63.
- 35. Wang, Yi*; Zhang, Hong-Xin; Sun, Yue-Ping; Liu, Zi-Xing; Liu, Xue-Song; Wang, Long; Lu, Shun-Yuan; Kong, Hui; Liu, Qiao-Ling; Li, Xi-Hua; Lu, Zhen-Yu; Chen, Sai-Juan; Chen, Zhu; Bao, Shi-San; Dai, Wei; Wang, Zhu-Gang#.Rig-I-/- mice develop colitis associated with downregulation of G alpha i2.CELL RESEARCH. 2007. 17(10):858-868.
- 36. Liu, Xue-Song*; Luo, Hui-Jun; Yang, Hua; Wang, Long; Kong, Hui; Jin, Yue-E; Wang, Fang; Gu, Ming-Min; Chen, Zhu; Lu, Zhen-Yu; Wang, Zhu-Gang#.Palladin regulates cell and extracellular matrix interaction through maintaining normal actin cytoskeleton architecture and stabilizing beta1-integrin.JOURNAL OF CELLULAR BIOCHEMISTRY. 2007. 100(5):1288-1300.
- 37. Liu, Xue-Song*; Li, Xi-Hua; Wang, Yi; Shu, Run-Zhe; Wang, Long; Lu, Shun-Yuan; Kong, Hui; Jin, Yue-E; Zhang, Li-Jun; Fei, Jian; Chen, Sai-Juan; Chen, Zhu; Gu, Ming-Min; Lu, Zhen-Yu; Wang, Zhu-Gang#.Disruption of palladin leads to defects in definitive erythropoiesis by interfering with erythroblastic island formation in mouse fetal liver.BLOOD. 2007. 110(3):870-876.
- 38. Luo, HJ*; Liu, XS*; Wang, F; Huang, QH; Shen, SH; Wang, L; Xu, GJ; Sun, X; Kong, H; Gu, MM; Chen, SJ; Chen, Z; Wang, ZG#.Disruption of palladin results in neural tube closure defects in mice.MOLECULAR AND CELLULAR NEUROSCIENCE. 2005. 29(4):507-515.
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