Identification of SOX4 target genes using phylogenetic footprinting-based prediction from expression microarrays suggests that overexpression of SOX4 potentiates metastasis in hepatocellular carcinoma

Oncogene

Volumn 27, Issue 42, 2008, Pages 5578-5589

  Liao, Y L ^a   Sun, Y M ^b   Chau, G Y ^c   Chau, Y P ^a   Lai, T C ^d   Wang, J L ^d   Horng, J T ^b   Hsiao, M ^d   Tsou, A P ^a  

^a NATIONAL YANG MING UNIVERSITY   (Taiwan)

^b NATIONAL CENTRAL UNIVERSITY   (Taiwan)

^c TAIPEI VETERANS GENERAL HOSPITAL   (Taiwan)

^d GENOMICS RESEARCH CENTER   (Taiwan)

Author keywords

HCC metastasis; SOX4; Synexpression; Target prediction

Indexed keywords

CHEMOTACTIC FACTOR; NEUROPILIN 1; RNA; SEMAPHORIN 3C; TRANSCRIPTION FACTOR SOX4; UNCLASSIFIED DRUG;

ANIMAL EXPERIMENT; ANIMAL MODEL; ANIMAL TISSUE; ARTICLE; BINDING SITE; CANCER CELL CULTURE; CANCER GROWTH; CARCINOGENESIS; CELL MIGRATION; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; DNA FOOTPRINTING; GENE CONTROL; GENE FUNCTION; GENE LOCUS; GENE OVEREXPRESSION; GENE TARGETING; GENETIC ANALYSIS; HUMAN; HUMAN CELL; IN VIVO STUDY; LIVER CELL CARCINOMA; METASTASIS; MICROARRAY ANALYSIS; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PREDICTION; PRIORITY JOURNAL; RNA INTERFERENCE;

ANIMALS; CARCINOMA, HEPATOCELLULAR; CELL LINE, TUMOR; CELL MOVEMENT; CHROMATIN IMMUNOPRECIPITATION; GENE EXPRESSION PROFILING; HUMANS; LIVER NEOPLASMS; MICE; NEOPLASM INVASIVENESS; NEOPLASM METASTASIS; NEUROPILIN-1; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHYLOGENY; RNA, SMALL INTERFERING; SEMAPHORINS; SOXC TRANSCRIPTION FACTORS;

EID: 52149109119     PISSN: 09509232     EISSN: 14765594     Source Type: Journal    
DOI: 10.1038/onc.2008.168     Document Type: Article

References (45)

1. Aaboe M, Birkenkamp-Demtroder K, Wiuf C, Sorensen FB, Thykjaer T, Sauter G et al. (2006). SOX4 expression in bladder carcinoma: clinical aspects and in vitro functional characterization. Cancer Res 66: 3434-3442.
2. Attia MA, Weiss DW. (1966). Immunology of spontaneous mammary carcinoma in mice. V. Acquired tumor resistance and enhancement in strain A mice infected with mammary tumor virus. Cancer Res 26: 1787-1800.
3. Bielenberg DR, Pettaway CA, Takashima S, Klagsbrun M. (2006). Neuropilins in neoplasms: expression, regulation, and function. Exp Cell Res 312: 584-593.
4. Bowles J, Schepers G, Koopman P. (2000). Phylogeny of the SOX family of developmental transcription factors based on sequence and structural indicators. Dev Biol 227: 239-255.
5. Chau GY, Lee AF, Tsay SH, Ke YR, Kao HL, Wong FH et al. (2007). Clinicopathological significance of survivin expression in patients with hepatocellular carcinoma. Histopathology 51: 204-218.
6. Chen X, Cheung ST, So S, Fan ST, Barry C, Higgins J et al. (2002). Gene expression patterns in human liver cancers. Mol Biol Cell 13: 1929-1939.
7. Cheung M, bu-Elmagd M, Clevers H, Scotting PJ. (2000). Roles of Sox4 in central nervous system development. Brain Res Mol Brain Res 79: 180-191.
8. El-Serag HB, Rudolph KL. (2007). Hepatocellular carcinoma: epidemiology and molecular carcinogenesis. Gastroenterology 132: 2557-2576.
9. Fickett JW, Wasserman WW. (2000). Discovery and modeling of transcriptional regulatory regions. Curr Opin Biotechnol 11: 19-24.
10. Geijsen N, Uings IJ, Pals C, Armstrong J, McKinnon M, Raaijmakers JA et al. (2001). Cytokine-specific transcriptional regulation through an IL-5Ralpha interacting protein. Science 293: 1136-1138.
11. Gonthier B, Nasarre C, Roth L, Perraut M, Thomasset N, Roussel G et al. (2007). Functional interaction between matrix metalloproteinase-3 and semaphorin-3C during cortical axonal growth and guidance. Cereb Cortex 17: 1712-1721.
12. Grizzi F, Franceschini B, Hamrick C, Frezza EE, Cobos E, Chiriva-Internati M. (2007). Usefulness of cancer-testis antigens as biomarkers for the diagnosis and treatment of hepatocellular carcinoma. J Transl Med 5: 3.
13. Guan KL, Rao Y. (2003). Signalling mechanisms mediating neuronal responses to guidance cues. Nat Rev Neurosci 4: 941-956.
14. Hardison RC, Oeltjen J, Miller W. (1997). Long human-mouse sequence alignments reveal novel regulatory elements: a reason to sequence the mouse genome. Genome Res 7: 959-966.
15. He Z, Tessier-Lavigne M. (1997). Neuropilin is a receptor for the axonal chemorepellent Semaphorin III. Cell 90: 739-751.
16. Herman JG, Meadows GG. (2007). Increased class 3 semaphorin expression modulates the invasive and adhesive properties of prostate cancer cells. Int J Oncol 30: 1231-1238.
17. Hong TM, Chen YL, Wu YY, Yuan A, Chao YC, Chung YC et al. (2007). Targeting neuropilin 1 as an antitumor strategy in lung cancer. Clin Cancer Res 13: 4759-4768.
18. Hunt SM, Clarke CL. (1999). Expression and hormonal regulation of the Sox4 gene in mouse female reproductive tissues. Biol Reprod 61: 476-481.
19. Hur EH, Hur W, Choi JY, Kim IK, Kim HY, Yoon SK et al. (2004). Functional identification of the pro-apoptotic effector domain in human Sox4. Biochem Biophys Res Commun 325: 59-67.
20. Kamachi Y, Uchikawa M, Kondoh H. (2000). Pairing SOX off: with partners in the regulation of embryonic development. Trends Genet 16: 182-187.
21. Kang Y, Siegel PM, Shu W, Drobnjak M, Kakonen SM, Cordon-Cardo C et al. (2003). A multigenic program mediating breast cancer metastasis to bone. Cancer Cell 3: 537-549.
22. Karaulanov E, Knochel W, Niehrs C. (2004). Transcriptional regulation of BMP4 synexpression in transgenic Xenopus. EMBO J 23: 844-856.
23. Kim Y, Sills RC, Houle CD. (2005). Overview of the molecular biology of hepatocellular neoplasms and hepatoblastomas of the mouse liver. Toxicol Pathol 33: 175-180.
24. Lee YC, Tang YC, Chen YH, Wong CM, Tsou AP. (2003). Selenite-induced survival of HuH7 hepatoma cells involves activation of focal adhesion kinase-phosphatidylinositol 3-kinase-Akt pathway and Rac1. J Biol Chem 278: 39615-39624.
25. Liu P, Ramachandran S, Ali SM, Scharer CD, Laycock N, Dalton WB et al. (2006). Sex-determining region Y box 4 is a transforming oncogene in human prostate cancer cells. Cancer Res 66: 4011-4019.
26. Lu YS, Kashida Y, Kulp SK, Wang YC, Wang D, Hung JH et al. (2007). Efficacy of a novel histone deacetylase inhibitor in murine models of hepatocellular carcinoma. Hepatology 46: 1119-1130.
27. Maes T, Barcelo A, Buesa C. (2002). Neuron navigator: a human gene family with homology to unc-53, a cell guidance gene from Caenorhabditis elegans. Genomics 80: 21-30.
28. McCracken S, Kim CS, Xu Y, Minden M, Miyamoto NG. (1997). An alternative pathway for expression of p56lck from type I promoter transcripts in colon carcinoma. Oncogene 15: 2929-2937.
29. Mertin S, McDowall SG, Harley VR. (1999). The DNA-binding specificity of SOX9 and other SOX proteins. Nucleic Acids Res 27: 1359-1364.
30. Minn AJ, Gupta GP, Siegel PM, Bos PD, Shu W, Giri DD et al. (2005). Genes that mediate breast cancer metastasis to lung. Nature 436: 518-524.
31. Nelson JD, Denisenko O, Sova P, Bomsztyk K. (2006). Fast chromatin immunoprecipitation assay. Nucleic Acids Res 34: e2.
32. Niehrs C, Pollet N. (1999). Synexpression groups in eukaryotes. Nature 402: 483-487.
33. Paget S. (1889). The distribution of secondary growth in cancer of the breast. Lancet 1: 571-573.
34. Pramoonjago P, Baras AS, Moskaluk CA. (2006). Knockdown of Sox4 expression by RNAi induces apoptosis in ACC3 cells. Oncogene 25: 5626-5639.
35. Remenyi A, Scholer HR, Wilmanns M. (2004). Combinatorial control of gene expression. Nat Struct Mol Biol 11: 812-815.
36. Schilham MW, Oosterwegel MA, Moerer P, Ya J, de Boer PA, van de WM et al. (1996). Defects in cardiac outflow tract formation and pro-B-lymphocyte expansion in mice lacking Sox-4. Nature 380: 711-714.
37. Shouval D, Schuger L, Levij IS, Reid LM, Neeman Z, Shafritz DA. (1988). Comparative morphology and tumourigenicity of human hepatocellular carcinoma cell lines in athymic rats and mice. Virchows Arch A Pathol Anat Histopathol 412: 595-606.
38. Tang ZY, Ye SL, Liu YK, Qin LX, Sun HC, Ye QH et al. (2004). A decade's studies on metastasis of hepatocellular carcinoma. J Cancer Res Clin Oncol 130: 187-196.
39. Tavazoie SF, Alarcón C, Oskarsson T, Padua D, Wang Q, Bos PD et al. (2008). Endogenous human microRNAs that suppress breast cancer metastasis. Nature 451: 147-152.
40. van de WM, Oosterwegel M, van NK, Clevers H. (1993). Sox-4, an Sry-like HMG box protein, is a transcriptional activator in lymphocytes. EMBO J 12: 3847-3854.
41. Wasserman WW, Palumbo M, Thompson W, Fickett JW, Lawrence CE. (2000). Human-mouse genome comparisons to locate regulatory sites. Nat Genet 26: 225-228.
42. Wilson M, Koopman P. (2002). Matching SOX: partner proteins and co-factors of the SOX family of transcriptional regulators. Curr Opin Genet Dev 12: 441-446.
43. Wotton D, Lake RA, Farr CJ, Owen MJ. (1995). The high mobility group transcription factor, SOX4, transactivates the human CD2 enhancer. J Biol Chem 270: 7515-7522.
44. Ya J, Schilham MW, de Boer PA, Moorman AF, Clevers H, Lamers WH. (1998). Sox4-deficiency syndrome in mice is an animal model for common trunk. Circ Res 83: 986-994.
45. Ye QH, Qin LX, Forgues M, He P, Kim JW, Peng AC et al. (2003). Predicting hepatitis B virus-positive metastatic hepatocellular carcinomas using gene expression profiling and supervised machine learning. Nat Med 9: 416-423.