Identification of Upstream Transcriptional Regulators of Ischemic Cardiomyopathy Using Cardiac RNA-Seq Meta-Analysis

Int J Mol Sci. 2020 May 14;21(10):3472. doi: 10.3390/ijms21103472.


Ischemic cardiomyopathy (ICM), characterized by pre-existing myocardial infarction or severe coronary artery disease, is the major cause of heart failure (HF). Identification of novel transcriptional regulators in ischemic HF can provide important biomarkers for developing new diagnostic and therapeutic strategies. In this study, we used four RNA-seq datasets from four different studies, including 41 ICM and 42 non-failing control (NF) samples of human left ventricle tissues, to perform the first RNA-seq meta-analysis in the field of clinical ICM, in order to identify important transcriptional regulators and their targeted genes involved in ICM. Our meta-analysis identified 911 differentially expressed genes (DEGs) with 582 downregulated and 329 upregulated. Interestingly, 54 new DEGs were detected only by meta-analysis but not in individual datasets. Upstream regulator analysis through Ingenuity Pathway Analysis (IPA) identified three key transcriptional regulators. TBX5 was identified as the only inhibited regulator (z-score = -2.89). F2R and SFRP4 were identified as the activated regulators (z-scores = 2.56 and 2.00, respectively). Multiple downstream genes regulated by TBX5, F2R, and SFRP4 were involved in ICM-related diseases such as HF and arrhythmia. Overall, our study is the first to perform an RNA-seq meta-analysis for clinical ICM and provides robust candidate genes, including three key transcriptional regulators, for future diagnostic and therapeutic applications in ischemic heart failure.

Keywords: RNA-seq; heart failure; ischemic cardiomyopathy; meta-analysis; transcriptional regulators.

Publication types

  • Meta-Analysis

MeSH terms

  • Cardiomyopathies / genetics*
  • Cardiomyopathies / pathology
  • Female
  • Gene Expression Profiling
  • Gene Expression Regulation / genetics
  • Heart Ventricles / metabolism
  • Heart Ventricles / pathology
  • Humans
  • Male
  • Myocardial Ischemia / genetics*
  • Myocardial Ischemia / pathology
  • Myocardium / metabolism*
  • RNA-Seq
  • Transcriptome / genetics*