MicroRNA and transcription factor mediated regulatory network analysis reveals critical regulators and regulatory modules in myocardial infarction

PLoS One. 2015 Aug 10;10(8):e0135339. doi: 10.1371/journal.pone.0135339. eCollection 2015.

Abstract

Myocardial infarction (MI) is a severe coronary artery disease and a leading cause of mortality and morbidity worldwide. However, the molecular mechanisms of MI have yet to be fully elucidated. In this study, we compiled MI-related genes, MI-related microRNAs (miRNAs) and known human transcription factors (TFs), and we then identified 1,232 feed-forward loops (FFLs) among these miRNAs, TFs and their co-regulated target genes through integrating target prediction. By merging these FFLs, the first miRNA and TF mediated regulatory network for MI was constructed, from which four regulators (SP1, ESR1, miR-21-5p and miR-155-5p) and three regulatory modules that might play crucial roles in MI were then identified. Furthermore, based on the miRNA and TF mediated regulatory network and literature survey, we proposed a pathway model for miR-21-5p, the miR-29 family and SP1 to demonstrate their potential co-regulatory mechanisms in cardiac fibrosis, apoptosis and angiogenesis. The majority of the regulatory relations in the model were confirmed by previous studies, which demonstrated the reliability and validity of this miRNA and TF mediated regulatory network. Our study will aid in deciphering the complex regulatory mechanisms involved in MI and provide putative therapeutic targets for MI.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology
  • Feedback, Physiological
  • Gene Expression Profiling
  • Gene Expression Regulation
  • Gene Regulatory Networks*
  • Humans
  • MicroRNAs / genetics*
  • MicroRNAs / metabolism
  • Models, Genetic*
  • Myocardial Infarction / genetics*
  • Myocardial Infarction / metabolism
  • Myocardial Infarction / pathology
  • Reproducibility of Results
  • Signal Transduction
  • Transcription Factors / genetics*
  • Transcription Factors / metabolism

Substances

  • MicroRNAs
  • Transcription Factors

Grants and funding

This work was supported in part by the National High Technology Research and Development Program of China [863 Program, Grant Nos. 2014AA021102], the National Program on Key Basic Research Project [973 Program, Grant Nos. 2014CB910504], the National Natural Science Foundation of China [Grant Nos. 61473106], the Natural Science Foundation of Heilongjiang Province, China (Grant No. QC2013C019) and the Science Foundation of Heilongjiang Provincial Health Department (Grant Nos. 2013126).