Asian Pacific Journal of Cancer Prevention

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

DOI QR Code

Regulatory Network of MicroRNAs, Host Genes, Target Genes and Transcription Factors in Human Esophageal Squamous Cell Carcinoma

  • Wang, Tian-Yan (College of Software Engineering, Jilin University) ;
  • Xu, Zhi-Wen (College of Computer Science and Technology, Jilin University) ;
  • Wang, Kun-Hao (College of Computer Science and Technology, Jilin University) ;
  • Wang, Ning (College of Computer Science and Technology, Jilin University)
  • Published : 2015.05.18
Download PDF
⟨ Previous Next ⟩

Abstract

Abnormally expressed microRNAs (miRNAs) and genes have been found to play key roles in esophageal squamous cell carcinoma (ESCC), but little is known about the underlying mechanisms. The aim of this paper was to assess inter-relationships and the regulatory mechanisms of ESCC through a network-based approach. We built three regulatory networks: an abnormally expressed network, a related network and a global network. Unlike previous examples, containing information only on genes or miRNAs, the prime focus was on relationships. It is worth noting that abnormally expressed network emerged as a fault map of ESCC. Theoretically, ESCC might be treated and prevented by correcting the included errors. In addition, the predicted transcription factors (TFs) obtained by the P-match method also warrant further study. Our results may further guide gene therapy researchers in the study of ESCC.

Keywords

References

  1. Baskerville S, Bartel DP (2005). Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA, 11, 241 7. https://doi.org/10.1261/rna.7240905
  2. Chekmenev DS, Haid C, Kel AE (2005). P-Match: transcription factor binding site search by combining patterns and weight matrices. Nucleic Acids Res, 33, 432-7. https://doi.org/10.1093/nar/gki441
  3. Chen ZL, Zhao XH, Wang JW, et al (2011). microRNA-92a promotes lymph node metastasis of human esophageal squamous cell carcinoma via E-cadherin. J Biol Chem, 286, 10725-34. https://doi.org/10.1074/jbc.M110.165654
  4. Chu EC, Tarnawski AS (2004). PTEN regulatory functions in tumor suppression and cell biology. Med Sci Monit, 10, 235-41.
  5. Fujita PA, Rhead B, Zweig AS, et al (2011). The UCSC genome browser database: update 2011. Nucleic Acids Res, 39, 876-82. https://doi.org/10.1093/nar/gkq963
  6. Hall-Glenn F, Lyons KM (2011). Roles for CCN2 in normal physiological processes. Cell Mol Life Sci, 68, 3209-17. https://doi.org/10.1007/s00018-011-0782-7
  7. Harata K, Ishiguro H, Kuwabara Y, et al (2010). MicroRNA-34b has an oncogenic role in esophageal squamous cell carcinoma. Oncol Lett, 1, 685-9.
  8. Hsu SD, Lin FM, Wu WY, et al (2011). miRTarBase: a database curates experimentally validated microRNA-target interactions. Nucleic Acids Res, 39, 163-9. https://doi.org/10.1093/nar/gkq1107
  9. Huang K, Chen L, Zhang J, et al (2014). Elevated p53 expression levels correlate with tumor progression and poor prognosis in patients exhibiting esophageal squamous cell carcinoma. Oncol Lett, 8, 1441-6.
  10. Jiang Q, Wang Y, Hao Y, et al (2009). miR2Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res, 37, 98-104.
  11. Jing JX, Wang Y, Xu XQ, et al (2014). Tumor markers for diagnosis, monitoring of recurrence and prognosis in patients with upper gastrointestinal tract cancer. Asian Pac J Cancer Prev, 15, 10267-72.
  12. Jun JI, Lau LF (2011). Taking aim at the extracellular matrix: CCN proteins as emerging therapeutic targets. Nat Rev Drug Discov, 10, 945-63. https://doi.org/10.1038/nrd3599
  13. Kanehisa M, Goto S (2000). KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res, 28, 27-30. https://doi.org/10.1093/nar/28.1.27
  14. Kozomara A, Griffiths-Jones S (2011). miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res, 39, 152-7.
  15. Kubota S, Takigawa M (2011). The role of CCN2 in cartilage and bone development. J Cell Commun Signal, 5, 209-17. https://doi.org/10.1007/s12079-011-0123-5
  16. Lee KW, Kim JH, Han S, et al (2012). Twist1 is an independent prognostic factor of esophageal squamous cell carcinoma and associated with its epithelial-mesenchymal transition. Ann Surg Oncol, 19, 326-35. https://doi.org/10.1245/s10434-011-1867-0
  17. Li J, Xu ZW, Wang KH, et al (2013). The network about microRNAs and genes in retinoblastoma. Asian Pac J Cancer Prev, 14, 6631-6. https://doi.org/10.7314/APJCP.2013.14.11.6631
  18. Li Y, Qiu C, Tu J, et al (2014). HMDD v2.0: a database for experimentally supported human microRNA and disease associations. Nucleic Acids Res, 42, 1070-4. https://doi.org/10.1093/nar/gkt1023
  19. Papadopoulos GL, Reczko M, SimECsis VA, Sethupathy P, Hatzigeorgiou AG (2009). The database of experimentally supported targets: a functional update of TarBase. Nucleic Acids Res, 37, 155-8. https://doi.org/10.1093/nar/gkn809
  20. Rodriguez A, Griffiths-Jones S, Ashurst JL, Bradley A (2004). Identification of mammalian microRNA host genes and transcription units. Genome Res, 14, 1902-10. https://doi.org/10.1101/gr.2722704
  21. Safran M, Dalah I, Alexander J, et al (2010). GeneCards version 3: the human gene integrator. Database, 2010, baq020.
  22. Sakai NS, Samia-Aly E, Barbera M, Fitzgerald RC (2013). A review of the current understanding and clinical utility of miRNAs in esophageal cancer. Semin Cancer Biol, 23, 512-21. https://doi.org/10.1016/j.semcancer.2013.08.005
  23. Tran DH, Satou K, Ho TB, Pham TH (2010). Computational discovery of miR TF regulatory modules in human genome. Bioinformation, 4, 371-7. https://doi.org/10.6026/97320630004371
  24. Wang J, Lu M, Qiu C, Cui Q (2010). TransmiR: a transcription factor-microRNA regulation database. Nucleic Acids Res, 38, 119-22.
  25. Wang L, Che XJ, Wang N, Li J (2014). Regulatory network analysis of microRNAs and genes in neuroblastoma. Asian Pac J Cancer Prev, 15, 7645-52. https://doi.org/10.7314/APJCP.2014.15.18.7645
  26. Xu X, Chen Z, Zhao X, et al (2012). MicroRNA-25 promotes cell migration and invasion in esophageal squamous cell carcinoma. Biochem Biophys Res Commun, 421, 640-5. https://doi.org/10.1016/j.bbrc.2012.03.048
  27. Zhang B, Xu ZW, Wang KH, et al (2013). Complex regulatory network of microRNAs, transcription factors, gene alterations in adrenocortical cancer. Asian Pac J Cancer Prev, 14, 2265-8. https://doi.org/10.7314/APJCP.2013.14.4.2265
  28. Zhang F, Yang Z, Cao M, et al (2014). MiR-203 suppresses tumor growth and invasion and down-regulates MiR-21 expression through repressing Ran in esophageal cancer. Cancer Lett, 342, 121-9. https://doi.org/10.1016/j.canlet.2013.08.037
  29. Zhou Y, Hong L (2013). Prediction value of miR-483 and miR-214 in prognosis and multidrug resistance of esophageal squamous cell carcinoma. Genet Test Mol Biomarkers, 17, 470-4. https://doi.org/10.1089/gtmb.2012.0518

Cited by

  1. B signaling in esophageal squamous cell carcinoma vol.6, pp.6, 2017, https://doi.org/10.1002/cam4.1068