Asian Pacific Journal of Cancer Prevention

Asian Pacific Journal of Cancer Prevention (아시아태평양암예방학회)
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Network Analysis of microRNAs, Genes and their Regulation in Mantle Cell Lymphoma

  • Deng, Si-Yu (College of Computer Science and Technology, Jilin University) ;
  • Guo, Xiao-Xin (College of Computer Science and Technology, Jilin University) ;
  • Wang, Ning (College of Computer Science and Technology, Jilin University) ;
  • Wang, Kun-Hao (College of Computer Science and Technology, Jilin University) ;
  • Wang, Shang (College of Computer Science and Technology, Jilin University)
  • Published : 2015.02.25
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Abstract

The pathogenesis of mantle cell lymphoma, a special subtype of lymphoma that is invasive and indolent and has a median survival of 3 to 4 years, is still partially unexplained. Much research about genes and miRNAs has been conducted in recent years, but interactions and regulatory relations of genetic elements which may play a vital role in genesis of MCL have attracted only limited attention. The present study concentrated on regulatory relations about genes and miRNAs contributing to MCL pathogenesis. Numerous experimentally validated raw data were organized into three topology networks, comprising differentially expressed, associated and global examples. Comparison of similarities and dissimilarities of the three regulating networks, paired with the analysis of the interactions between pairs of elements in every network, revealed that the differentially expressed network illuminated the carcinogenicity mechanism of MCL and the related network further described the regulatory relations involved, including prevention, diagnosis, development and therapy. Three kinds of regulatory relations for host genes including miRNAs, miRNAs targeting genes and genes regulating miRNAs were concluded macroscopically. Regulation of the differentially expressed miRNAs was also analyzed, in terms of abnormal gene expression affecting the MCL pathogenesis. Special regulatory relations were uncovered. For example, auto-regulatory loops were found in the three topology networks, key pathways of the nodes being highlighted. The present study focused on a novel point of view revealing important influencing factors for MCL pathogenesis.

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References

  1. Akyure N, Drakos E, et al (2010). Differential expression of CKS-1B in typical and blastoid variants of mantle cell lymphoma. Hum Pathol, 41, 1448-55. https://doi.org/10.1016/j.humpath.2010.04.001
  2. 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
  3. Chekmenev DS1, 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
  4. Dreszer TR, Karolchik D, Zweig AS, et al (2012). The UCSC genome browser database: extensions and updates 2011. Nucleic Acids Res, 40, 918-23. https://doi.org/10.1093/nar/gkr1055
  5. 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.
  6. Kozomara A, Griffiths-Jones S (2011). miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res, 39, 152-7.
  7. Kavitha N,Vijayarathna S, et al (2014). MicroRNAs: biogenesis, roles for carcinogenesis and as potential biomarkers for cancer diagnosis and prognosis. Asian Pac J Cancer Prev, 15, 7489-97. https://doi.org/10.7314/APJCP.2014.15.18.7489
  8. Libermann TA, Zerbini LF, et al (2006). Targeting transcription factors for cancer gene therapy, Curr Gene Ther, 6, 17-33. https://doi.org/10.2174/156652306775515501
  9. Liu H1, Wang B, Lin J, Zhao L (2014). microRNA-29b: an emerging player in human cancer. Asian Pac J Cancer Prev, 15, 9059-64. https://doi.org/10.7314/APJCP.2014.15.21.9059
  10. Meissner B, Kridel R, Lim RS, et al (2013). The E3 ubiquitin ligase UBR5 is recurrently mutated in mantle cell lymphoma. Blood, 121, 3161-4. https://doi.org/10.1182/blood-2013-01-478834
  11. Mu YP, Tang S, Sun WJ, et al (2014). Association of miR-193b down-regulation and miR-196a up-regulation with clinicopathological features and prognosis in gastric cancer. Asian Pac J Cancer Prev, 15, 8893-900. https://doi.org/10.7314/APJCP.2014.15.20.8893
  12. Saj A, Lai EC (2011). Control of microRNA biogenesis and transcription by cell signaling pathways. Curr Opin Genet Dev, 21, 504-10. https://doi.org/10.1016/j.gde.2011.04.010
  13. Wang J, Lu M, et al (2010). TransmiR: a transcription factormicroRNA regulation database. Nucleic Acids Res, 38, 119-22.

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