Gene expression network analysis reveals new transcriptional regulators as novel factors in human ischemic cardiomyopathy

BMC Med Genomics. 2015 Mar 29;8:14. doi: 10.1186/s12920-015-0088-y.

Abstract

Background: Ischemic cardiomyopathy (ICM) is characterized by transcriptomic changes that alter cellular processes leading to decreased cardiac output. Because the molecular network of ICM is largely unknown, the aim of this study was to characterize the role of new transcriptional regulators in the molecular mechanisms underlying the responses to ischemia.

Methods: Myocardial tissue explants from ICM patients and control (CNT) subjects were analyzed by RNA-Sequencing (RNA-Seq) and quantitative Real-Time PCR.

Results: Enrichment analysis of the ICM transcriptomic profile allowed the characterization of novel master regulators. We found that the expression of the transcriptional regulators SP100 (-1.5-fold, p < 0.05), CITED2 (-3.8-fold, p < 0.05), CEBPD (-4.9-fold, p < 0.05) and BCL3 (-3.3-fold, p < 0.05) were lower in ICM than in CNT. To gain insights into the molecular network defined by the transcription factors, we identified CEBPD, BCL3, and HIF1A target genes in the RNA-Seq datasets. We further characterized the biological processes of the target genes by gene ontology annotation. Our results suggest that CEBPD-inducible genes with roles in the inhibition of apoptosis are downregulated and that BCL3-repressible genes are involved in the regulation of cellular metabolism in ICM. Moreover, our results suggest that CITED2 downregulation causes increased expression of HIF1A target genes. Functional analysis of HIF1A target genes revealed that hypoxic and stress response genes are activated in ICM. Finally, we found a significant correlation between the mRNA levels of BCL3 and the mRNA levels of both CEBPD (r = 0.73, p < 0.001) and CITED2 (r = 0.56, p < 0.05). Interestingly, CITED2 mRNA levels are directly related to ejection fraction (EF) (r = 0.54, p < 0.05).

Conclusions: Our data indicate that changes in the expression of SP100, CITED2, CEBPD, and BCL3 affect their transcription regulatory networks, which subsequently alter a number of biological processes in ICM patients. The relationship between CITED2 mRNA levels and EF emphasizes the importance of this transcription factor in ICM. Moreover, our findings identify new mechanisms used to interpret gene expression changes in ICM and provide valuable resources for further investigation of the molecular basis of human cardiac ischemic response.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Aged
  • Antigens, Nuclear / metabolism
  • Apoptosis
  • Autoantigens / metabolism
  • B-Cell Lymphoma 3 Protein
  • CCAAT-Enhancer-Binding Protein-delta / metabolism
  • Cardiomyopathies / genetics*
  • Cardiomyopathies / metabolism
  • Female
  • Gene Expression Profiling*
  • Gene Expression Regulation
  • Humans
  • Male
  • Middle Aged
  • Myocardial Ischemia / genetics*
  • Myocardial Ischemia / metabolism
  • Myocardium / pathology
  • Principal Component Analysis
  • Proto-Oncogene Proteins / metabolism
  • Real-Time Polymerase Chain Reaction
  • Repressor Proteins / metabolism
  • Sequence Analysis, RNA
  • Trans-Activators / metabolism
  • Transcription Factors / metabolism*
  • Transcription, Genetic*
  • Transcriptome

Substances

  • Antigens, Nuclear
  • Autoantigens
  • B-Cell Lymphoma 3 Protein
  • BCL3 protein, human
  • CEBPD protein, human
  • CITED2 protein, human
  • Proto-Oncogene Proteins
  • Repressor Proteins
  • Trans-Activators
  • Transcription Factors
  • Sp100 protein, human
  • CCAAT-Enhancer-Binding Protein-delta