A systems biology approach reveals common metastatic pathways in osteosarcoma

BMC Systems Biology

Volumn 6, Issue , 2012, Pages

  Flores, Ricardo J ^a,b   Li, Yiting ^a,b   Yu, Alexander ^a,b   Shen, Jianhe ^a,b   Rao, Pulivarthi H ^a,b   Lau, Serrine S ^c   Vannucci, Marina ^d   Lau, Ching C ^a,b   Man, Tsz Kwong ^a,b  

^a TEXAS CHILDREN S HOSPITAL   (United States)

^b BAYLOR COLLEGE OF MEDICINE   (United States)

^c UNIVERSITY OF ARIZONA   (United States)

^d Rice University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GLYCOGEN; GLYCOPROTEIN; MESSENGER RNA; TRANSCRIPTOME; TUMOR NECROSIS FACTOR ALPHA; WHEAT GERM AGGLUTININ; WNT PROTEIN;

ANIMAL; ARTICLE; CYTOSKELETON; GENE EXPRESSION REGULATION; GENETICS; HUMAN; LUNG TUMOR; METABOLISM; METASTASIS; METHODOLOGY; MOUSE; OSTEOSARCOMA; PATHOLOGY; PROTEOMICS; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY; TUMOR CELL LINE;

ANIMALS; CELL LINE, TUMOR; CYTOSKELETON; GENE EXPRESSION REGULATION, NEOPLASTIC; GLYCOGEN; GLYCOPROTEINS; HUMANS; LUNG NEOPLASMS; MICE; NEOPLASM METASTASIS; OSTEOSARCOMA; PROTEOMICS; RNA, MESSENGER; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY; TRANSCRIPTOME; TUMOR NECROSIS FACTOR-ALPHA; WHEAT GERM AGGLUTININS; WNT PROTEINS;

EID: 84861436481     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-6-50     Document Type: Article

References (72)

1. Mirabello L, Troisi RJ, Savage SA. Osteosarcoma incidence and survival rates from 1973 to 2004: data from the Surveillance, Epidemiology, and End Results Program. Cancer 2009, 115(7):1531-1543.
2. Petrilli AS, et al. Results of the Brazilian Osteosarcoma Treatment Group Studies III and IV: prognostic factors and impact on survival. J Clin Oncol 2006, 24(7):1161-1168.
3. Meyers PA, et al. Osteogenic sarcoma with clinically detectable metastasis at initial presentation. J Clin Oncol 1993, 11(3):449-453.
4. Bjornland K, et al. Matrix metalloproteinases participate in osteosarcoma invasion. J Surg Res 2005, 127(2):151-156.
5. Khanna C, et al. Metastasis-associated differences in gene expression in a murine model of osteosarcoma. Cancer Res 2001, 61(9):3750-3759.
6. Kleijn M, et al. Regulation of translation initiation factors by signal transduction. Eur J Biochem 1998, 253(3):531-544.
7. Gygi SP, et al. Correlation between protein and mRNA abundance in yeast. Mol Cell Biol 1999, 19(3):1720-1730.
8. Chen G, et al. Discordant protein and mRNA expression in lung adenocarcinomas. Mol Cell Proteomics 2002, 1(4):304-313.
9. Man TK, et al. Optimising the use of TRIzol-extracted proteins in surface enhanced laser desorption/ ionization (SELDI) analysis. Proteome Sci 2006, 4:3.
10. Luu HH, et al. An orthotopic model of human osteosarcoma growth and spontaneous pulmonary metastasis. Clin Exp Metastasis 2005, 22(4):319-329.
11. Chen X, et al. Establishment and characterization of human osteosarcoma cell lines with different pulmonary metastatic potentials. Cytotechnology 2009, 61(1-2):37-44.
12. Kimura K, et al. Establishment of human osteosarcoma cell lines with high metastatic potential to lungs and their utilities for therapeutic studies on metastatic osteosarcoma. Clin Exp Metastasis 2002, 19(6):477-485.
13. Nakano T, et al. Biological properties and gene expression associated with metastatic potential of human osteosarcoma. Clin Exp Metastasis 2003, 20(7):665-674.
14. Jia SF, Worth LL, Kleinerman ES. A nude mouse model of human osteosarcoma lung metastases for evaluating new therapeutic strategies. Clin Exp Metastasis 1999, 17(6):501-506.
15. Rhim JS, et al. Characterization of human cells transformed in vitro by N-methyl-N'-nitro-N-nitrosoguanidine. Int J Cancer 1977, 19(4):505-510.
16. Fogh J, Fogh JM, Orfeo T. One hundred and twenty-seven cultured human tumor cell lines producing tumors in nude mice. J Natl Cancer Inst 1977, 59(1):221-226.
17. Li Y, et al. Detection and verification of glycosylation patterns of glycoproteins from clinical specimens using lectin microarrays and lectin-based immunosorbent assays. Anal Chem 2011, 83(22):8509-16.
18. Theriault C, et al. MUC16 (CA125) regulates epithelial ovarian cancer cell growth, tumorigenesis and metastasis. Gynecol Oncol 2011, 121(3):434-43.
19. Narimatsu H. Construction of a human glycogene library and comprehensive functional analysis. Glycoconj J 2004, 21(1-2):17-24.
20. Zhang B, et al. Detecting differential and correlated protein expression in label-free shotgun proteomics. J Proteome Res 2006, 5(11):2909-18.
21. Benjamini Y, Hochberg Y. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J R Stat Soc 1995, Series B(57):289-300.
22. Gupta R, Jung E, Brunak S. NetNGlyc 1.0 Server 2004, Center For Biological Sequence Analysis, Techical University of Denmark, Kongens Lyngby, Denmark, available at http://www.cbs.dtu.dk/services/NetNGlyc/.
23. Gupta R, Brunak S. Prediction of glycosylation across the human proteome and the correlation to protein function. Pac Symp Biocomput 2002, 7:310-22.
24. Qiu J, et al. Occurrence of autoantibodies to annexin I, 14-3-3 theta and LAMR1 in prediagnostic lung cancer sera. J Clin Oncol 2008, 26(31):5060-6.
25. Li Z, et al. Role of 14-3-3sigma in poor prognosis and in radiation and drug resistance of human pancreatic cancers. BMC Cancer 2010, 10:598.
26. Tomaino B, et al. Circulating autoantibodies to phosphorylated alpha-enolase are a hallmark of pancreatic cancer. J Proteome Res 2011, 10(1):105-12.
27. Ishiwata T, Matsuda Y, Naito Z. Nestin in gastrointestinal and other cancers: effects on cells and tumor angiogenesis. World J Gastroenterol 2011, 17(4):409-18.
28. Nijkamp MM, et al. Expression of E-cadherin and vimentin correlates with metastasis formation in head and neck squamous cell carcinoma patients. Radiother Oncol 2011, 99(3):344-8.
29. Vellaichamy A, et al. "Topological significance" analysis of gene expression and proteomic profiles from prostate cancer cells reveals key mechanisms of androgen response. PLoS One 2010, 5(6):e10936.
30. Dezso Z, et al. Identifying disease-specific genes based on their topological significance in protein networks. BMC Syst Biol 2009, 3:36.
31. Kvinlaug BT, et al. Common and Overlapping Oncogenic Pathways Contribute to the Evolution of Acute Myeloid Leukemias. Cancer Res 2011, 71(12):4117-4129.
32. Daves MH, et al. Meta-analysis of multiple microarray datasets reveals a common gene signature of metastasis in solid tumors. BMC Med Genomics 2011, 4(1):56.
33. Yilmaz M, Christofori G. Mechanisms of motility in metastasizing cells. Mol Cancer Res 2010, 8(5):629-42.
34. Zhang K, et al. Slug enhances invasion ability of pancreatic cancer cells through upregulation of matrix metalloproteinase-9 and actin cytoskeleton remodeling. Lab Invest 2011, 91(3):426-38.
35. Zhang H, et al. Engagement of I-Branching beta}-1, 6-N-Acetylglucosaminyltransferase 2 in Breast Cancer Metastasis and TGF-{beta Signaling. Cancer Res 2011, 71(14):4846-4856.
36. Takebe N, Warren RQ, Ivy SP. Breast cancer growth and metastasis: interplay between cancer stem cells, embryonic signaling pathways and epithelial-to-mesenchymal transition. Breast Cancer Res 2011, 13(3):211.
37. Letson GD, Muro-Cacho CA. Genetic and molecular abnormalities in tumors of the bone and soft tissues. Cancer Control 2001, 8(3):239-51.
38. Sudoyo AW, Hardi F. Cytogenetics in solid tumors: lessons from the Philadelphia Chromosome. Acta Med Indones 2011, 43(1):68-73.
39. Espada J, et al. Wnt signalling and cancer stem cells. Clin Transl Oncol 2009, 11(7):411-27.
40. Guo Y, et al. Blocking Wnt/LRP5 signaling by a soluble receptor modulates the epithelial to mesenchymal transition and suppresses met and metalloproteinases in osteosarcoma Saos-2 cells. J Orthop Res 2007, 25(7):964-71.
41. Qiao L, et al. Dkk-1 secreted by mesenchymal stem cells inhibits growth of breast cancer cells via depression of Wnt signalling. Cancer Lett 2008, 269(1):67-77.
42. Vijayakumar S, et al. High-frequency canonical Wnt activation in multiple sarcoma subtypes drives proliferation through a TCF/beta-catenin target gene, CDC25A. Cancer Cell 2011, 19(5):601-12.
43. Polakis P. The many ways of Wnt in cancer. Curr Opin Genet Dev 2007, 17(1):45-51.
44. Reya T, Clevers H. Wnt signalling in stem cells and cancer. Nature 2005, 434(7035):843-50.
45. Haydon RC, et al. Cytoplasmic and/or nuclear accumulation of the beta-catenin protein is a frequent event in human osteosarcoma. Int J Cancer 2002, 102(4):338-42.
46. Hoang BH, et al. Expression of LDL receptor-related protein 5 (LRP5) as a novel marker for disease progression in high-grade osteosarcoma. Int J Cancer 2004, 109(1):106-11.
47. Kansara M, et al. Wnt inhibitory factor 1 is epigenetically silenced in human osteosarcoma, and targeted disruption accelerates osteosarcomagenesis in mice. J Clin Invest 2009, 119(4):837-51.
48. Rubin EM, et al. Wnt inhibitory factor 1 decreases tumorigenesis and metastasis in osteosarcoma. Mol Cancer Ther 2010, 9(3):731-41.
49. Muller A, et al. Involvement of chemokine receptors in breast cancer metastasis. Nature 2001, 410(6824):50-6.
50. Singh S, et al. CXCR1 and CXCR2 enhances human melanoma tumourigenesis, growth and invasion. Br J Cancer 2009, 100(10):1638-46.
51. Vicari AP, Caux C. Chemokines in cancer. Cytokine Growth Factor Rev 2002, 13(2):143-54.
52. Jiang P, Enomoto A, Takahashi M. Cell biology of the movement of breast cancer cells: intracellular signalling and the actin cytoskeleton. Cancer Lett 2009, 284(2):122-30.
53. Clarke NW, Hart CA, Brown MD. Molecular mechanisms of metastasis in prostate cancer. Asian J Androl 2009, 11(1):57-67.
54. von Luettichau I, et al. A complex pattern of chemokine receptor expression is seen in osteosarcoma. BMC Cancer 2008, 8:23.
55. Li Y, et al. Elevated expression of CXC chemokines in pediatric osteosarcoma patients. Cancer 2011, 117(1):207-17.
56. Kim SY, et al. Inhibition of the CXCR4/CXCL12 chemokine pathway reduces the development of murine pulmonary metastases. Clin Exp Metastasis 2008, 25(3):201-11.
57. Kaji H, et al. Lectin affinity capture, isotope-coded tagging and mass spectrometry to identify N-linked glycoproteins. Nat Biotechnol 2003, 21(6):667-72.
58. Kaji H, et al. Mass spectrometric identification of N-linked glycopeptides using lectin-mediated affinity capture and glycosylation site-specific stable isotope tagging. Nat Protoc 2006, 1(6):3019-27.
59. Nunomura K, et al. Cell surface labeling and mass spectrometry reveal diversity of cell surface markers and signaling molecules expressed in undifferentiated mouse embryonic stem cells. Mol Cell Proteomics 2005, 4(12):1968-76.
60. Wollscheid B, et al. Mass-spectrometric identification and relative quantification of N-linked cell surface glycoproteins. Nat Biotechnol 2009, 27(4):378-86.
61. Wu CC, et al. Candidate serological biomarkers for cancer identified from the secretomes of 23 cancer cell lines and the human protein atlas. Mol Cell Proteomics 2010, 9(6):1100-17.
62. Kulasingam V, Diamandis EP. Strategies for discovering novel cancer biomarkers through utilization of emerging technologies. Nat Clin Pract Oncol 2008, 5(10):588-99.
63. Irizarry RA, et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003, 4(2):249-64.
64. Bolstad BM, et al. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003, 19(2):185-93.
65. Irizarry RA, et al. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 2003, 31(4):e15.
66. Craig P, Conrad H, Robert G. affyQCReport: QC Report Generation for affyBatch objects. R package version 1.32.0
67. Kennedy RE, Archer KJ, Miles MF. Empirical validation of the S-Score algorithm in the analysis of gene expression data. BMC Bioinforma 2006, 7:154.
68. Kennedy RE, et al. SScore: an R package for detecting differential gene expression without gene expression summaries. Bioinformatics 2006, 22(10):1272-4.
69. Nancy LA, et al. Proteomic characterization of wheat amyloplasts using identification of proteins by tandem mass spectrometry. Proteomics 2002, 2(9):1156-1168.
70. Yates JR, et al. Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database. Anal Chem 1995, 67(8):1426-36.
71. Nesvizhskii AI, et al. A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem 2003, 75(17):4646-58.
72. Edgar R, Domrachev M, Lash AE. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 2002, 30(1):207-10.