Multi-omics analysis reveals regulators of the response to PDGF-BB treatment in pulmonary artery smooth muscle cells

BMC Genomics. 2016 Oct 6;17(1):781. doi: 10.1186/s12864-016-3122-3.

Abstract

Background: Pulmonary arterial hypertension (PAH) is a lethal disease with pronounced narrowing of pulmonary vessels due to abnormal cell proliferation. The platelet-derived growth factor BB (PDGF-BB) is well known as a potent mitogen for smooth muscle cell proliferation. To better understand how this growth factor regulates pulmonary arterial smooth muscle cells (PASMCs) proliferation, we sought to characterize the response to PDGF-BB stimulation at system-wide levels, including the transcriptome and proteome.

Results: In this study, we identified 1611 mRNAs (transcriptome), 207 proteins (proteome) differentially expressed in response to PDGF-BB stimulation in PASMCs based on RNA-sequencing and isobaric tags for relative and absolute quantification (iTRAQ) assay. Transcription factor (TF)-target network analysis revealed that PDGF-BB regulated gene expression potentially via TFs including HIF1A, JUN, EST1, ETS1, SMAD1, FOS, SP1, STAT1, LEF1 and CEBPB. Among them, SMAD1-involved BMPR2/SMADs axis plays a significant role in PAH development. Interestingly, we observed that the expression of BMPR2 was decreased in both mRNA and protein level in response to PDGF-BB. Further study revealed that BMPR2 is the direct target of miR-376b that is up-regulated upon PDGF-BB treatment. Finally, EdU incorporation assay showed that miR-376b promoted proliferation of PASMCs.

Conclusion: This integrated analysis of PDGF-BB-regulated transcriptome and proteome was performed for the first time in normal PASMCs, which revealed a crosstalk between PDGF signaling and BMPR2/SMADs axis. Further study demonstrated that PDGF-BB-induced miR-376b upregulation mediated the downregulation of BMPR2, which led to expression change of its downstream targets and promoted proliferation of PASMCs.

Keywords: BMPR2; Platelet-derived growth factor-BB (PDGF-BB); Pulmonary arterial hypertension (PAH); RNA sequencing; iTRAQ; miR-376b.

MeSH terms

  • Animals
  • Becaplermin
  • Cluster Analysis
  • Gene Expression Profiling / methods
  • Gene Expression Regulation
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Muscle, Smooth, Vascular / metabolism*
  • Myocytes, Smooth Muscle / drug effects*
  • Myocytes, Smooth Muscle / metabolism*
  • Proteomics / methods
  • Proto-Oncogene Proteins c-sis / pharmacology*
  • Pulmonary Artery / metabolism*
  • RNA Interference
  • Reproducibility of Results
  • Transcriptome

Substances

  • Proto-Oncogene Proteins c-sis
  • Becaplermin