Asian Pacific Journal of Cancer Prevention

Asian Pacific Journal of Cancer Prevention (아시아태평양암예방학회)
권호 표지
DOI QR코드

DOI QR Code

Shortest Path Analyses in the Protein-Protein Interaction Network of NGAL (Neutrophil Gelatinase-associated Lipocalin) Overexpression in Esophageal Squamous Cell Carcinoma

  • Du, Ze-Peng (Department of Pathology, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen University) ;
  • Wu, Bing-Li (Department of Biochemistry and Molecular Biology, Shantou University Medical College) ;
  • Wang, Shao-Hong (Department of Pathology, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen University) ;
  • Shen, Jin-Hui (Department of Pathology, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen University) ;
  • Lin, Xuan-Hao (Department of Pathology, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen University) ;
  • Zheng, Chun-Peng (Department of Oncology Surgery, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen University) ;
  • Wu, Zhi-Yong (Department of Oncology Surgery, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen University) ;
  • Qiu, Xiao-Yang (Department of Pathology, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen University) ;
  • Zhan, Xiao-Fen (Department of Pathology, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen University) ;
  • Xu, Li-Yan (Institute of Oncologic Pathology, Shantou University Medical College) ;
  • Li, En-Min (Department of Biochemistry and Molecular Biology, Shantou University Medical College)
  • Published : 2014.08.30
Download PDF
⟨ Previous Next ⟩

Abstract

NGAL (neutrophil gelatinase-associated lipocalin) is a novel cancer-related protein involves multiple functions in many cancers and other diseases. We previously overexpressed NGAL to analyze its role in esophageal squamous cell carcinoma (ESCC). In this study, a protein-protein interaction (PPI) was constructed and the shortest paths from NGAL to transcription factors in the network were analyzed. We found 28 shortest paths from NGAL to RELA, most of them obeying the principle of extracellular to cytoplasm, then nucleus. These shortest paths were also prioritized according to their normalized intensity from the microarray by the order of interaction cascades. A systems approach was developed in this study by linking differentially expressed genes with publicly available PPI data, Gene Ontology and subcellular localizaton for the integrated analyses. These shortest paths from NGAL to DEG transcription factors or other transcription factors in the PPI network provide important clues for future experimental identification of new pathways.

Keywords

References

  1. Abecassis I, Olofsson B, Schmid M, et al (2003). RhoA induces MMP-9 expression at CD44 lamellipodial focal complexes and promotes HMEC-1 cell invasion. Exp Cell Res, 291, 363-76. https://doi.org/10.1016/j.yexcr.2003.08.006
  2. Barsky A, Gardy JL, Hancock RE, et al (2007). Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation. Bioinformatics, 23, 1040-2. https://doi.org/10.1093/bioinformatics/btm057
  3. Chakraborty S, Kaur S, Guha S, et al (2012). The multifaceted roles of neutrophil gelatinase associated lipocalin (NGAL) in inflammation and cancer. Biochim Biophys Acta, 1826, 129-69.
  4. Chatr-Aryamontri A, Breitkreutz BJ, Heinicke S, et al (2013). The BioGRID interaction database: 2013 update. Nucleic Acids Res, 41, 816-23. https://doi.org/10.1093/nar/gks1158
  5. Csardi G, Nepusz T (2006). The igraph software package for complex network research. InterJournal Complex Systems, 5, 1695.
  6. Dijkstra E (1959). A note on two problems in connection with graphs. Numerische Mathematik, 1, 269-71. https://doi.org/10.1007/BF01386390
  7. Du ZP, Lv Z, Wu BL, et al (2011.) Neutrophil gelatinaseassociated lipocalin and its receptor: independent prognostic factors of oesophageal squamous cell carcinoma. J Clin Pathol, 64, 69-74. https://doi.org/10.1136/jcp.2010.083907
  8. Flower DR (1996). The lipocalin protein family: structure and function. Biochem J, 318, 1-14.
  9. Friedman A, Perrimon N (2007). Genetic screening for signal transduction in the era of network biology. Cell, 128, 225-31. https://doi.org/10.1016/j.cell.2007.01.007
  10. Goel R, Muthusamy B, Pandey A, et al (2011). Human protein reference database and human proteinpedia as discovery resources for molecular biotechnology. Mol Biotechnol, 48, 87-95. https://doi.org/10.1007/s12033-010-9336-8
  11. Hayden MS, Ghosh S (2008). Shared principles in NF-kappaB signaling. Cell, 132, 344-62. https://doi.org/10.1016/j.cell.2008.01.020
  12. Hu L, Hittelman W, Lu T, et al (2009). NGAL decreases E-cadherin mediated cell-cell adhesion and increases cell motility and invasion through Rac1 in colon carcinoma cells. Lab I nvest, 89, 531-48.
  13. Huang da W, Sherman BT, Lempicki RA (2009). Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res, 37, 1-13. https://doi.org/10.1093/nar/gkn923
  14. Jiang C, Xuan Z, Zhao F, et al (2007). TRED: a transcriptional regulatory element database, new entries and other development. Nucleic Acids Res, 35, 137-40.
  15. Kerrien S, Aranda B, Breuza L, et al (2012). The IntAct molecular interaction database in 2012. Nucleic Acids Res, 40, 841-6. https://doi.org/10.1093/nar/gkr1088
  16. Kumar G, Ranganathan S (2010). Network analysis of human protein location. BMC Bioinformatics, 11 Suppl 7, S9.
  17. Matys V, Fricke E, Geffers R, et al (2003). TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res, 31, 374-8. https://doi.org/10.1093/nar/gkg108
  18. Pan XH (2012). Pathway crosstalk analysis based on proteinprotein network analysis in ovarian cancer. Asian Pac J Cancer Prev, 13, 3905-9. https://doi.org/10.7314/APJCP.2012.13.8.3905
  19. Petrella BL, Armstrong DA, Vincenti MP (2011). CCAATenhancer- binding protein beta activation of MMP-1 gene expression in SW1353 cells: independent roles of extracellular signal-regulated and p90/ribosomal S6 kinases. J Cell Physiol, 226, 3349-54. https://doi.org/10.1002/jcp.22693
  20. Rees JR, Onwuegbusi BA, Save VE, et al (2006). In vivo and in vitro evidence for transforming growth factor-beta1- mediated epithelial to mesenchymal transition in esophageal adenocarcinoma. Cancer Res, 66, 9583-90. https://doi.org/10.1158/0008-5472.CAN-06-1842
  21. Smoot ME, Ono K, Ruscheinski J, et al (2011). Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics, 27, 431-2. https://doi.org/10.1093/bioinformatics/btq675
  22. Tong Z, Kunnumakkara AB, Wang H, et al (2008). Neutrophil gelatinase-associated lipocalin: a novel suppress or of invasion and angiogenesis in pancreatic cancer. Cancer Res, 68, 6100-8. https://doi.org/10.1158/0008-5472.CAN-08-0540
  23. Wang F, He W, Fanghui P, et al (2013). $NF-{\kappa}BP65$ promotes invasion and metastasis of oesophageal squamous cell cancer by regulating matrix metalloproteinase-9 and epithelial-tomesenchymal transition. Cell Biol Int, 37, 780-8. https://doi.org/10.1002/cbin.10089
  24. Wu J, Vallenius T, Ovaska K, et al (2009). Integrated network analysis platform for protein-protein interactions. Nat Methods, 6, 75-7. https://doi.org/10.1038/nmeth.1282
  25. Yan L, Borregaard N, Kjeldsen L, et al (2001). The high molecular weight urinary matrix metalloproteinase (MMP) activity is a complex of gelatinase B/MMP-9 and neutrophil gelatinase-associated lipocalin (NGAL). Modulation of MMP-9 activity by NGAL. J Biol Chem, 276, 37258-65. https://doi.org/10.1074/jbc.M106089200
  26. Yang J, Goetz D, Li JY, et al (2002). An iron delivery pathway mediated by a lipocalin. Mol Cell, 10, 1045-56. https://doi.org/10.1016/S1097-2765(02)00710-4
  27. Zhang H, Xu L, Xiao D, et al (2007) Up regulation of neutrophil gelatinase associated lipocalin in oesophageal squamous cell carcinoma: significant correlation with cell differentiation and tumour invasion. J Clin Pathol, 60, 555-61.
  28. Zhu XL, Ai ZH, Wang J, et al (2012). Weighted gene coexpression network analysis in identification of endometrial cancer prognosis markers. Asian Pac J Cancer Prev, 13, 4607-11. https://doi.org/10.7314/APJCP.2012.13.9.4607