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Xuedong LIU
Office Phone: 303 735 6161
E-mail: Xuedong.Liu@colorado.edu
FAX: 303 492 5894
Lab: Cristol Chemistry 365
Group Website: http://liulab.colorado.edu/
Ph.D.: University of Wisconsin-Madison, 1994
Postdoctoral Fellow: NIH Fellow at Whitehead Institute, 1995- 1998
US Army Breast Cancer Postdoctoral Fellow at MIT, 1998-2000
TGF-β signaling in normal and cancer cells
We aim to understand the role of transforming growth factor-β (TGF-β) signaling in normal and cancer cells. TGF-β is a multi-functional cytokine responsible for regulating growth and differentiation of a wide variety of cell types and tissues. It is a potent inhibitor of normal epithelial cell proliferation and possesses tumor suppressing activity. The majority of human tumors are of epithelial origin and their proliferation is no longer inhibited by TGF-β. This usually arises either from a loss of key signaling molecules in the TGF-β signal transduction pathway (e.g., TGF-β receptors), or from activation of oncogenes. TGF-β can positively regulate expression of many tumor suppressor genes which cause the cell to stop proliferation and yet negatively regulate expression of many protooncogenes/oncogenes which promote cell cycle progression. The action of TGF-β in normal epithelial cells is to downshift the engine that drives cell proliferation by shifting the balance of the activity of the oncogene and tumor suppressor gene.
TGF-β signals via two receptor Ser/Thr protein kinases, termed type I and type II TGF-β receptors. The type II receptor phosphorylates and activates the type I receptor, which then phosphorylates Smad2 or Smad3 within their C-terminal Ser-Ser-X-Ser motifs. Once activated, Smad2 or Smad3 associate with the shared signaling molecule Smad4, translocate to the nucleus and in concert with additional transcription factors alters the transcription of a large repertoire of genes. Although several key downstream targets that transduce the TGF-β signals from the cell surface to the nucleus have been identified, it remains to be determined how TGF-β can mediate myriad cellular responses and regulate so many important physiological processes. To address how TGF-β signaling could mediate such diverse effects, we use the two following approaches: 1) Find as yet unidentified molecules that may mediate diverse functions, and 2) understand how the TGF-β network behaves as a system, which may identify how known network components interact to produce unexpected emergent behavior. The principal methods used to achieve these aims include cDNA library screening for genes that mediate TGF-β resistance (Erickson et al., submitted), purification and identification by mass spectrometry of protein complexes associated with well-established signaling transducers (Knuesel et al., 2003, Zhu et al., 2006) and computational modeling of TGF-β/Smad signaling dynamics (Clarke et al., 2006).
Transcriptional regulation
Genome sequencing has revealed the basic molecular blueprint for diverse organisms. How such sequences give rise to the development and physiology of such organisms is of great interest. Many processes are regulated at the transcriptional level, which are mediated by transcription factor proteins that bind specific and distinct DNA sequences in the promoter and enhancer regions of genes. Predicting which transcription factors bind the promoters of genes of interest is crucial for understanding transcriptional regulation. We have developed a suite of computational tools, called GeneACT (http:// promoter.colorado.edu/geneact), for studying global transcriptional regulation. Recently we developed a new computational method called PRI (http://barcode.colorado.edu/pri/) which leads to identification of pattern-defined regulatory element in mammalian genome (Cheung et al., 2007).
Post-translational regulation
Proteins in the cell are subject to diverse covalent modifications that serve to alter their activity, localization, or turnover. Such modifications include ubiquitination and covalent attachment of ubiquitin-like molecules (e.g., SUMO or small ubiquitin-like modifier). We initially became interested in how these modifications regulate cell cycle proteins that could disrupt TGF-β signaling (Liu et al., 2000). We subsequently found further interplay between TGF-β signaling and protein degradation mechanisms (Wang et al., 2004, MacDonald et al., 2004). More recently, we have sought to determine the biochemical mechanisms by which E3 ligases mediate ubiquitination of their substrates (Wang et al., 2004, Ungermannova et al., 2005, Wang et al., 2005). We continue to pursue these studies using structural and biochemical techniques. In addition, recent studies were done to establish the functional importance of post-translational modifications on the activity of transcription factors. Here, muscle differentiation, which is largely driven through transcriptional regulation, was used as a model system (Riquelme et al., 2006, 2 separate publications). We have developed proteomics techniques for identification of mammalian protein complexes using tandem affinity purification (Knuesel et al., 2003, Zhu et al., 2007) and programmed data acquisition (PDA) and UBLfinder (http:// http://promoter.colorado.edu/ublfinder/about.html) to identify post-translational modication of proteins using mass spectrometry (Knuesel et al., 2005).
Cell cycle function
A hallmark of tumor cells is an inability to control their proliferation, which implies that these cells are capable of bypassing cell cycle checkpoints and regulation by tumor suppressor signaling pathways such as TGF-β signaling. Combating cancer therefore depends on understanding the molecular basis by which tumor cells evade these growth control mechanisms. Recently initiated studies seek to identify genes important for mitotic checkpoint function in normal and cancer cell lines.
Selected Publications
1. Cheung TH, Barthel KK, Kwan YL, Liu X. (2007) Identifying pattern-defined regulatory islands in mammalian genomes. Proc Natl Acad Sci U S A. 2007 Jun 12;104(24):10116-21. http://barcode.colorado.edu/pri/
2. Zhu, S., Wang, W., Clarke, D. C. and Liu, X. (2007). Activation of Mps1 promotes TGF-beta independent Smad signaling. J Biol Chem. pdf
3. Cheung, T. H., Kwan, Y. L., Hamady, M. and Liu, X. (2006). Unraveling trancriptional control and cis-regulatory codes using the software suite GeneACT. Genome Biology. 7: r97. promoter.colorado.edu/geneact
4. Riquelme, C., Barthel, K. K. and Liu, X. (2006). SUMO-1 modification of MEF2A regulates its transcriptional activity. J Cell Mol Med. 10: 132-44.
5. Riquelme, C., Barthel, K. K., Qin, X. F. and Liu, X. (2006). Ubc9 expression is essential for myotube formation in C2C12. Exp Cell Res. 312: 2132-41.
6. Clarke, D. C., Betterton, M. D. and Liu, X. (2006). Systems theory of Smad signalling. Systems Biology (Stevenage). 153: 409-466. Supplementary Materials
7. Kfir, S., Ehrlich, M., Goldshmid, A., Liu, X., Kloog, Y. and Henis, Y. I. (2005). Pathway- and expression level-dependent effects of oncogenic N-Ras: p27(Kip1) mislocalization by the Ral-GEF pathway and Erk-mediated interference with Smad signaling. Mol Cell Biol. 25: 8239-50.
8. Knuesel, M., Cheung, H. T., Hamady, M., Barthel, K. K. and Liu, X. (2005). A method of mapping protein sumoylation sites by mass spectrometry using a modified small ubiquitin-like modifier 1 (SUMO-1) and a computational program. Mol Cell Proteomics. 4: 1626-36.
9. Wang, W., Nacusi, L., Sheaff, R. J. and Liu, X. (2005). Ubiquitination of p21Cip1/WAF1 by SCFSkp2: substrate requirement and ubiquitination site selection. Biochemistry. 44: 14553-64.
10. Ungermannova, D., Gao, Y. and Liu, X. (2005). Ubiquitination of p27Kip1 requires physical interaction with cyclin E and probable phosphate recognition by SKP2. J Biol Chem. 280: 30301-9.
11. Liang, M., Liang, Y. Y., Wrighton, K., Ungermannova, D., Wang, X. P., Brunicardi, F. C., Liu, X., Feng, X. H. and Lin, X. (2004). Ubiquitination and proteolysis of cancer-derived Smad4 mutants by SCFSkp2. Mol Cell Biol. 24: 7524-37.
12. Royer, Y., Menu, C., Liu, X. and Constantinescu, S. N. (2004). High-throughput gateway bicistronic retroviral vectors for stable expression in mammalian cells: exploring the biologic effects of STAT5 overexpression. DNA Cell Biol. 23: 355-65.
13. Macdonald, M., Wan, Y., Wang, W., Roberts, E., Cheung, T. H., Erickson, R., Knuesel, M. T. and Liu, X. (2004). Control of cell cycle-dependent degradation of c-Ski proto-oncoprotein by Cdc34. Oncogene. 23: 5643-53.
14. Wang, W., Ungermannova, D., Jin, J., Harper, J. W. and Liu, X. (2004). Negative regulation of SCFSkp2 ubiquitin ligase by TGF-beta signaling. Oncogene. 23: 1064-75.
15. Wang, W., Ungermannova, D., Chen, L. and Liu, X. (2004). Molecular and biochemical characterization of the Skp2-Cks1 binding interface. J Biol Chem. 279: 51362-9.
16. Knuesel, M., Wan, Y., Xiao, Z., Holinger, E., Lowe, N., Wang, W. and Liu, X. (2003). Identification of novel protein-protein interactions using a versatile mammalian tandem affinity purification expression system. Mol Cell Proteomics. 2: 1225-33.
17. Wang, W., Ungermannova, D., Chen, L. and Liu, X. (2003). A negatively charged amino acid in Skp2 is required for Skp2-Cks1 interaction and ubiquitination of p27Kip1. J Biol Chem. 278: 32390-6.
18. Fu M, Zhang J, Zhu X, Myles DE, Wilson TM, Liu X, Chen YE. PPARgamma inhibits TGF-ß -induced connective tissue growth factor expression in human aortic smooth muscle cells by interfering with Smad3. J. Biol. Chem. 276:45888-94, 2001.
19. *Blobe, G. C., *Liu, X., Fang, S. J., How, T. and Lodish, H. F. (2001). A novel mechanism for regulating transforming growth factor beta (TGF-beta) signaling. Functional modulation of type III TGF-beta receptor expression through interaction with the PDZ domain protein, GIPC. J Biol Chem. 276: 39608-17. * Co-first author
20. Wan, Y., Liu, X. and Kirschner, M. W. (2001). The anaphase-promoting complex mediates TGF-beta signaling by targeting SnoN for destruction. Mol Cell. 8: 1027-39.
21. Liu, X., Sun, Y., Weinberg, R. A. and Lodish, H. F. (2001). Ski/Sno and TGF-beta signaling. Cytokine Growth Factor Rev. 12: 1-8.
22. Liu, X., Sun, Y., Ehrlich, M., Lu, T., Kloog, Y., Weinberg, R. A., Lodish, H. F. and Henis, Y. I. (2000). Disruption of TGF-beta growth inhibition by oncogenic ras is linked to p27Kip1 mislocalization. Oncogene. 19: 5926-
23. Xiao, Z., Liu, X., Henis, Y. I. and Lodish, H. F. (2000). A distinct nuclear localization signal in the N terminus of Smad 3 determines its ligand-induced nuclear translocation. Proc Natl Acad Sci U S A. 97: 7853-8.
24. Xiao, Z., Liu, X. and Lodish, H. F. (2000). Importin beta mediates nuclear translocation of Smad 3. J Biol Chem. 275: 23425-8.
25. Liu, X., Constantinescu, S. N., Sun, Y., Bogan, J. S., Hirsch, D., Weinberg, R. A. and Lodish, H. F. (2000). Generation of mammalian cells stably expressing multiple genes at predetermined levels. Anal Biochem. 280: 20-8.
26. Sun, Y., Liu, X., Ng-Eaton, E., Lodish, H. F. and Weinberg, R. A. (1999). SnoN and Ski protooncoproteins are rapidly degraded in response to transforming growth factor beta signaling. Proc Natl Acad Sci U S A. 96: 12442-7.
27. *Sun, Y., *Liu, X., Eaton, E. N., Lane, W. S., Lodish, H. F. and Weinberg, R. A. (1999). Interaction of the Ski oncoprotein with Smad3 regulates TGF-beta signaling. Mol Cell. 4: 499-509. * Co-first author
28. Constantinescu, S. N., Liu, X., Beyer, W., Fallon, A., Shekar, S., Henis, Y. I., Smith, S. O. and Lodish, H. F. (1999). Activation of the erythropoietin receptor by the gp55-P viral envelope protein is determined by a single amino acid in its transmembrane domain. Embo J. 18: 3334-
29. Wells, R. G., Gilboa, L., Sun, Y., Liu, X., Henis, Y. I. and Lodish, H. F. (1999). Transforming growth factor-beta induces formation of a dithiothreitol-resistant type I/Type II receptor complex in live cells. J Biol Chem. 274: 5716-22.
30. Hua, X., Liu, X., Ansari, D. O. and Lodish, H. F. (1998). Synergistic cooperation of TFE3 and smad proteins in TGF-beta-induced transcription of the plasminogen activator inhibitor-1 gene. Genes Dev. 12: 3084-95.
31. Constantinescu, S. N., Wu, H., Liu, X., Beyer, W., Fallon, A. and Lodish, H. F. (1998). The anemic Friend virus gp55 envelope protein induces erythroid differentiation in fetal liver colony-forming units-erythroid. Blood. 91: 1163-72.
32. Kuo, J. S., Patel, M., Gamse, J., Merzdorf, C., Liu, X., Apekin, V. and Sive, H. (1998). opl: a zinc finger protein that regulates neural determination and patterning in Xenopus. Development. 125: 2867-2882.
33. Liu, X., Sun, Y., Constantinescu, S. N., Karam, E., Weinberg, R. A. and Lodish, H. F. (1997). Transforming growth factor beta-induced phosphorylation of Smad3 is required for growth inhibition and transcriptional induction in epithelial cells. Proc Natl Acad Sci U S A. 94: 10669-74.
34. Johnston, S. X., Liu, X., Zuo, F., Eisenbraun, T., Wiley, S., Kraus, R. and Mertz, J. E. (1997). Estrogen-related receptor-1 functionally binds as a monomer to extended half-site sequences including ones contained within estrogen-response elements. Molecular Endocrinology. 11: 342-352.
35. Liu, X. and Mertz, J. E. (1996). Sequence of the polypyrimidine tract of the 3'-terminal 3' splicing signal can affect intron-dependent pre-mRNA processing in vivo. Nucleic Acids Res. 24: 1765-73.
36. Liu, X. and Mertz, J. E. (1995). HnRNP L binds a cis-acting RNA sequence element that enables intron-dependent gene expression. Genes Dev. 9: 1766-80.
37. Liu, X. and Mertz, J. E. (1993). Polyadenylation site selection cannot occur in vivo after excision of the 3'-terminal intron. Nucleic Acids Res. 21: 5256-63.
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