Table of Contents Author Guidelines Submit a Manuscript
BioMed Research International
Volume 2014 (2014), Article ID 594350, 12 pages
http://dx.doi.org/10.1155/2014/594350
Research Article

Identification of MicroRNA as Sepsis Biomarker Based on miRNAs Regulatory Network Analysis

1Systems Sepsis Biology Team, Soochow University Affiliated Children’s Hospital, Suzhou 215003, China
2Center for Systems Biology, Soochow University, Suzhou 215006, China
3Suzhou Zhengxing Translational Biomedical Informatics Ltd., Taicang 215400, China
4Taicang Center for Translational Bioinformatics, Taicang 215400, China

Received 17 January 2014; Accepted 3 March 2014; Published 6 April 2014

Academic Editor: Junfeng Xia

Copyright © 2014 Jie Huang et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. F. B. Mayr, S. Yende, and D. C. Angus, “Epidemiology of severe sepsis,” Virulence, vol. 5, no. 1, 2013. View at Google Scholar
  2. M. M. Levy, M. P. Fink, J. C. Marshall et al., “2001 SCCM/ESICM/ACCP/ATS/SIS International Sepsis Definitions Conference,” Critical Care Medicine, vol. 31, no. 4, pp. 1250–1256, 2003. View at Publisher · View at Google Scholar · View at Scopus
  3. S. E. Calvano, W. Xiao, D. R. Richards et al., “A network-based analysis of systemic inflammation in humans,” Nature, vol. 437, no. 7061, pp. 1032–1037, 2005. View at Publisher · View at Google Scholar · View at Scopus
  4. D. C. Angus, W. T. Linde-Zwirble, J. Lidicker, G. Clermont, J. Carcillo, and M. R. Pinsky, “Epidemiology of severe sepsis in the United States: analysis of incidence, outcome, and associated costs of care,” Critical Care Medicine, vol. 29, no. 7, pp. 1303–1310, 2001. View at Google Scholar · View at Scopus
  5. A. Kumar, D. Roberts, K. E. Wood et al., “Duration of hypotension before initiation of effective antimicrobial therapy is the critical determinant of survival in human septic shock,” Critical Care Medicine, vol. 34, no. 6, pp. 1589–1596, 2006. View at Publisher · View at Google Scholar · View at Scopus
  6. D. C. Angus, “The lingering consequences of sepsis: a hidden public health disaster?” The Journal of the American Medical Association, vol. 304, no. 16, pp. 1833–1834, 2010. View at Publisher · View at Google Scholar · View at Scopus
  7. C. Pierrakos and J.-L. Vincent, “Sepsis biomarkers: a review,” Critical Care, vol. 14, no. 1, article R15, 2010. View at Publisher · View at Google Scholar · View at Scopus
  8. J. D. Faix, “Biomarkers of sepsis,” Critical Reviews in Clinical Laboratory Sciences, vol. 50, no. 1, pp. 23–36, 2013. View at Google Scholar
  9. T. Chan and F. Gu, “Early diagnosis of sepsis using serum biomarkers,” Expert Review of Molecular Diagnostics, vol. 11, no. 5, pp. 487–496, 2011. View at Publisher · View at Google Scholar · View at Scopus
  10. V. Ambros, “The functions of animal microRNAs,” Nature, vol. 431, no. 7006, pp. 350–355, 2004. View at Publisher · View at Google Scholar · View at Scopus
  11. D. P. Bartel, “MicroRNAs: genomics, Biogenesis, Mechanism, and Function,” Cell, vol. 116, no. 2, pp. 281–297, 2004. View at Publisher · View at Google Scholar · View at Scopus
  12. M. A. Cortez and G. A. Calin, “MicroRNA identification in plasma and serum: a new tool to diagnose and monitor diseases,” Expert Opinion on Biological Therapy, vol. 9, no. 6, pp. 703–711, 2009. View at Publisher · View at Google Scholar · View at Scopus
  13. Y. Li, Z. Zhang, F. Liu, W. Vongsangnak, Q. Jing, and B. Shen, “Performance comparison and evaluation of software tools for microRNA deep-sequencing data analysis,,” Nucleic Acids Research, vol. 40, no. 10, pp. 4298–4305, 2012. View at Google Scholar
  14. R. Ranjha and J. Paul, “Micro-RNAs in inflammatory diseases and as a link between inflammation and cancer,” Inflammation Research, vol. 62, no. 4, pp. 343–355, 2013. View at Publisher · View at Google Scholar
  15. S. Akkina and B. N. Becker, “MicroRNAs in kidney function and disease,” Translational Research, vol. 157, no. 4, pp. 236–240, 2011. View at Publisher · View at Google Scholar · View at Scopus
  16. M. V. Iorio, M. Ferracin, C.-G. Liu et al., “MicroRNA gene expression deregulation in human breast cancer,” Cancer Research, vol. 65, no. 16, pp. 7065–7070, 2005. View at Publisher · View at Google Scholar · View at Scopus
  17. M. Zhao, J. Sun, and Z. Zhao, “Synergetic regulatory networks mediated by oncogene-driven microRNAs and transcription factors in serous ovarian cancer,” Molecular BioSystems, vol. 9, no. 12, pp. 3187–3198, 2013. View at Publisher · View at Google Scholar
  18. H. J. Wang, P. J. Zhang, W. J. Chen et al., “Four serum microRNAs identified as diagnostic biomarkers of sepsis,” Journal of Trauma and Acute Care Surgery, vol. 73, no. 4, pp. 850–854, 2012. View at Publisher · View at Google Scholar
  19. H. Wang, P. Zhang, W. Chen, D. Feng, Y. Jia, and L. X. Xie, “Evidence for serum miR-15a and miR-16 levels as biomarkers that distinguish sepsis from systemic inflammatory response syndrome in human subjects,” Clinical Chemistry and Laboratory Medicine, vol. 50, no. 8, pp. 1423–1428, 2012. View at Google Scholar
  20. H. Wang, P. Zhang, W. Chen, D. Feng, Y. Jia, and L. Xie, “Serum microRNA signatures identified by Solexa sequencing predict sepsis patients' mortality: a prospective observational study,” PLoS ONE, vol. 7, no. 6, Article ID e38885, 2012. View at Google Scholar
  21. Y. P. Chen, X. Jin, Z. Xiang, S. H. Chen, and Y. M. Li, “Circulating MicroRNAs as potential biomarkers for alcoholic steatohepatitis,” Liver International, vol. 33, no. 8, pp. 1257–1265, 2013. View at Google Scholar
  22. S. Rahmann, M. Martina, J. H. Schultec, J. Kösterb, T. Marschalle, and A. Schrammb, “Identifying transcriptional miRNA biomarkers by integrating high-throughput sequencing and real-time PCR data,” Methods, vol. 59, no. 1, pp. 154–163, 2013. View at Publisher · View at Google Scholar
  23. H. Si, X. Sun, Y. Chen et al., “Circulating microRNA-2a and microRNA-21 as novel minimally invasive biomarkers for primary breast cancer,” Journal of Cancer Research and Clinical Oncology, vol. 139, no. 2, pp. 223–229, 2013. View at Google Scholar
  24. H. Wang, W. Peng, X. Ouyang, W. Li, and Y. Da, “Circulating microRNAs as candidate biomarkers in patients with systemic lupus erythematosus,” Translational Research, vol. 160, no. 3, pp. 198–206, 2012. View at Publisher · View at Google Scholar
  25. Y. Wang, M. Chen, Z. Tao, Q. Hua, S. Chen, and B. Xiao, “Identification of predictive biomarkers for early diagnosis of larynx carcinoma based on microRNA expression data,” Cancer Genetics, vol. 206, no. 9-10, pp. 340–346, 2013. View at Google Scholar
  26. H. Zhao, J. Shen, L. Medico, D. Wang, C. B. Ambrosone, and S. Liu, “A pilot study of circulating miRNAs as potential biomarkers of early stage breast cancer,” PLoS ONE, vol. 5, no. 10, Article ID e13735, 2010. View at Publisher · View at Google Scholar · View at Scopus
  27. G. Zheng, Y. Xiong, and W. Xu al, “A two-microRNA signature as a potential biomarker for early gastric cancer,” Oncology Letters, vol. 7, no. 3, pp. 679–684, 2014. View at Google Scholar
  28. W. Zhang, J. Zang, and X. Jinge al, “Identification of candidate miRNA biomarkers from miRNA regulatory network with application to prostate cancer,” Journal of Translational Medicine, vol. 12, article 66, 2014. View at Publisher · View at Google Scholar
  29. J. Chen, D. Zhang, W. Zhang et al., “Clear cell renal cell carcinoma associated microRNA expression signatures identified by an integrated bioinformatics analysis,,” Journal of Translational Medicine, vol. 11, article169, 2013. View at Publisher · View at Google Scholar
  30. S. Griffiths-Jones, H. K. Saini, S. Van Dongen, and A. J. Enright, “miRBase: tools for microRNA genomics,” Nucleic Acids Research, vol. 36, no. 1, pp. D154–D158, 2008. View at Publisher · View at Google Scholar · View at Scopus
  31. C. Vasilescu, S. Rossi, M. Shimizu et al., “MicroRNA fingerprints identify miR-150 as a plasma prognostic marker in patients with sepsis,” PLoS ONE, vol. 4, no. 10, Article ID e7405, 2009. View at Publisher · View at Google Scholar · View at Scopus
  32. V. Chongsuvivatwong, “Epicalc: epidemiological calculator,” R package version 2. 15. 1. 0, 2012, http://CRAN.R-project.org/package=epicalc.
  33. F. Xiao, Z. Zuo, G. Cai, S. Kang, X. Gao, and T. Li, “miRecords: an integrated resource for microRNA-target interactions,” Nucleic Acids Research, vol. 37, no. 1, pp. D105–D110, 2009. View at Publisher · View at Google Scholar · View at Scopus
  34. P. Sethupathy, B. Corda, and A. G. Hatzigeorgiou, “TarBase: a comprehensive database of experimentally supported animal microRNA targets,” RNA, vol. 12, no. 2, pp. 192–197, 2006. View at Publisher · View at Google Scholar · View at Scopus
  35. Q. Jiang, Y. Wang, Y. Hao et al., “miR2Disease: a manually curated database for microRNA deregulation in human disease,” Nucleic Acids Research, vol. 37, no. 1, pp. D98–D104, 2009. View at Publisher · View at Google Scholar · View at Scopus
  36. S.-D. Hsu, F.-M. Lin, W.-Y. Wu et al., “miRTarBase: a database curates experimentally validated microRNA-target interactions,” Nucleic Acids Research, vol. 39, no. 1, pp. D163–D169, 2011. View at Publisher · View at Google Scholar · View at Scopus
  37. V. A. Gennarino, M. Sardiello, R. Avellino et al., “MicroRNA target prediction by expression analysis of host genes,” Genome Research, vol. 19, no. 3, pp. 481–490, 2009. View at Publisher · View at Google Scholar · View at Scopus
  38. E. R. Gamazon, H.-K. Im, S. Duan et al., “ExprTarget: an integrative approach to predicting human microRNA targets,” PLoS ONE, vol. 5, no. 10, Article ID e13534, 2010. View at Publisher · View at Google Scholar · View at Scopus
  39. J.-H. Yang, J.-H. Li, P. Shao, H. Zhou, Y.-Q. Chen, and L.-H. Qu, “StarBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data,” Nucleic Acids Research, vol. 39, no. 1, pp. D202–D209, 2011. View at Publisher · View at Google Scholar · View at Scopus
  40. M. Ding, H. Wang, J. Chen, B. Shen, and Z. Xu, “Identification and functional annotation of genome-wide ER-regulated genes in breast cancer based on ChIP-Seq data,” Computational and Mathematical Methods in Medicine, vol. 2012, Article ID 568950, p. 10, 2012. View at Publisher · View at Google Scholar
  41. G. Liu, M. Ding, J. Chen et al., “Computational analysis of microRNA function in heart development,” Acta Biochimica et Biophysica Sinica, vol. 42, no. 9, pp. 662–670, 2010. View at Google Scholar
  42. Y. Tang, W. Yan, J. Chen, C. Luo, A. Kaipia, and B. Shen, “Identification of novel microRNA regulatory pathways associated with heterogeneous prostate cancer,” BMC Systems Biology, vol. 7, supplement 6, 2013. View at Google Scholar
  43. D. W. Huang, B. T. Sherman, and R. A. Lempicki, “Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources,” Nature Protocols, vol. 4, no. 1, pp. 44–57, 2009. View at Publisher · View at Google Scholar · View at Scopus
  44. D. Binns, E. Dimmer, R. Huntley, D. Barrell, C. O'Donovan, and R. Apweiler, “QuickGO: a web-based tool for gene ontology searching,” Bioinformatics, vol. 25, no. 22, pp. 3045–3046, 2009. View at Publisher · View at Google Scholar · View at Scopus
  45. J.-F. Wang, M.-L. Yu, G. Yu et al., “Serum miR-146a and miR-223 as potential new biomarkers for sepsis,” Biochemical and Biophysical Research Communications, vol. 394, no. 1, pp. 184–188, 2010. View at Publisher · View at Google Scholar · View at Scopus
  46. H. Wang, K. Meng, W. J. Chen, D. Feng, Y. Jia, and L. Xie, “Serum miR-574-5p: a prognostic predictor of sepsis patients,” Shock, vol. 37, no. 3, pp. 263–267, 2012. View at Publisher · View at Google Scholar · View at Scopus
  47. A. E. Pasquinelli, “MicroRNAs and their targets: recognition, regulation and an emerging reciprocal relationship,” Nature Reviews Genetics, vol. 13, no. 4, pp. 271–282, 2012. View at Publisher · View at Google Scholar · View at Scopus
  48. X. Lai, A. Bhattacharya, U. Schmitz, M. Kunz, J. Vera, and O. Wolkenhauer, “A Systems' Biology Approach to Study microRNA-mediated gene regulatory networks,” BioMed Research International:, vol. 2013, Article ID 703849, 15 pages, 2013. View at Publisher · View at Google Scholar
  49. B. Liu, J. Chen, and B. Shen, “Genome-wide analysis of the transcription factor binding preference of human bi-directional promoters and functional annotation of related gene pairs,” BMC Systems Biology, vol. 5, no. 1, article S2, 2011. View at Publisher · View at Google Scholar · View at Scopus
  50. Y. Wang, J. Chen, Q. Li et al., “Identifying novel prostate cancer associated pathways based on integrative microarray data analysis,” Computational Biology and Chemistry, vol. 35, no. 3, pp. 151–158, 2011. View at Publisher · View at Google Scholar · View at Scopus
  51. G. Ramachandran, “Gram-positive and gram-negative bacterial toxins in sepsis: a brief review,” Virulence, vol. 5, no. 1, 2013. View at Google Scholar
  52. R. S. Hotchkiss, P. E. Swanson, B. D. Freeman et al., “Apoptotic cell death in patients with sepsis, shock, and multiple organ dysfunction,” Critical Care Medicine, vol. 27, no. 7, pp. 1230–1251, 1999. View at Publisher · View at Google Scholar · View at Scopus
  53. U. Fiedler and H. G. Augustin, “Angiopoietins: a link between angiogenesis and inflammation,” Trends in Immunology, vol. 27, no. 12, pp. 552–558, 2006. View at Publisher · View at Google Scholar · View at Scopus
  54. P. M. Roger, H. Hyvernat, M. Ticchioni, G. Kumar, J. Dellamonica, and G. Bernardin, “The early phase of human sepsis is characterized by a combination of apoptosis and proliferation of T cells,” Journal of Critical Care, vol. 27, no. 4, pp. 384–393, 2012. View at Publisher · View at Google Scholar
  55. J.-L. Vincent, “Clinical sepsis and septic shock—definition, diagnosis and management principles,” Langenbeck's Archives of Surgery, vol. 393, no. 6, pp. 817–824, 2008. View at Publisher · View at Google Scholar · View at Scopus
  56. H. Liang and W.-H. Li, “MicroRNA regulation of human protein-protein interaction network,” RNA, vol. 13, no. 9, pp. 1402–1408, 2007. View at Publisher · View at Google Scholar · View at Scopus
  57. C.-W. Tseng, C.-C. Lin, C.-N. Chen, H.-C. Huang, and H.-F. Juan, “Integrative network analysis reveals active microRNAs and their functions in gastric cancer,” BMC Systems Biology, vol. 5, article 99, 2011. View at Publisher · View at Google Scholar · View at Scopus
  58. J. Wu, T. Vallenius, K. Ovaska, J. Westermarck, T. P. Mäkelä, and S. Hautaniemi, “Integrated network analysis platform for protein-protein interactions,” Nature Methods, vol. 6, no. 1, pp. 75–77, 2009. View at Publisher · View at Google Scholar · View at Scopus
  59. P. A. Ward, “Sepsis, apoptosis and complement,” Biochemical Pharmacology, vol. 76, no. 11, pp. 1383–1388, 2008. View at Publisher · View at Google Scholar · View at Scopus
  60. J. Rusiecka-ZióŁkowska, M. Walszewska, J. Stekla, and B. Szponar, “Role of endotoxin in pathomechanism of sepsis,” Polski Merkuriusz Lekarski, vol. 25, no. 147, pp. 260–265, 2008. View at Google Scholar · View at Scopus