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Series GSE115317 Query DataSets for GSE115317
Status Public on Sep 11, 2018
Title Coronary artery disease genes SMAD3 and TCF21 promote opposing interactive genetic programs that regulate smooth muscle cell differentiation and disease risk [ChIP-seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Third-party reanalysis
Summary Although numerous genetic loci have been associated with coronary artery disease (CAD) with genome wide association studies (GWAS), efforts are needed to identify the causal genes in these loci and link them into fundamental signaling pathways. Toward that end, experiments reported here extend our investigation of the disease mechanism of CAD associated gene SMAD3, a central transcriptional intermediate in the TGFb pathway, investigating its role in smooth muscle biology. In vitro studies in human coronary artery smooth muscle cells (HCASMC) revealed that SMAD3 modulates cell state decisions in this cell type, promoting expression of differentiation marker genes and migration while inhibiting proliferation. RNA and chromatin immunoprecipitation sequencing (ChIPseq) studies in HCASMC identified downstream genes that reside in pathways which mediate vascular development and disease processes, including those related to atherosclerosis pathophysiology, expanding understanding of the TGFb canonical pathway in this cell type. ChIPseq studies also found colocalization of SMAD3 binding in loci targeted by TCF21, a CAD associated transcription factor that has been shown to produce a CAD protective de-differentiation program in HCASMC. In loci where these factors are juxtaposed on DNA, SMAD3 binding was anti-correlated with TCF21, and increased in cells depleted of TCF21, as shown by ChIPseq and ChIP experiments. Further, reporter gene studies revealed that while SMAD3 increased transcription at a SERPINE1 enhancer, and this effect was blocked by TCF21. Together, these data suggest that SMAD3 regulation of gene expression is modulated by TCF21, through independent regulation of jointly occupied genes and through epigenetic and possibly direct protein-protein interactions. Finally, eQTL studies in HCASMC indicated that SMAD3 expression is directly associated with increased disease risk, opposing the known protective effect of TCF21. We propose that the pro-differentiation function of SMAD3 inhibits HCASMC dedifferentiation of these cells as they respond to vascular stresses and expand and migrate to stabilize the plaque, and that SMAD3 function is directly opposed at the transcriptional level by the disease protective expression of TCF21, which promotes dedifferentiation and phenotypic modulation.
 
Overall design Human coronary artery smooth muscle cells (HCASMC) grown in serum were evaluated with an antibody to SMAD3, or IgG control.

This series includes the re-analysis of GSM1246721. The processed data for this anti-SMAD3 ChIP sample in A549 cells are available at the foot of this record.
 
Contributor(s) Iyer D, Zhao Q, Quertermous T
Citation(s) 30307970
Submission date Jun 04, 2018
Last update date Mar 20, 2019
Contact name Thomas Quertermous
E-mail(s) tomq1@stanford.edu
Phone 650-723-5012
Organization name Stanford University
Department Medicine Cardiology
Lab Quertermous
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platforms (1)
GPL20795 HiSeq X Ten (Homo sapiens)
Samples (2)
GSM3175516 TQ324-SMAD3
GSM3175517 TQ325-IgG
This SubSeries is part of SuperSeries:
GSE115319 Coronary artery disease genes SMAD3 and TCF21 promote opposing interactive genetic programs that regulate smooth muscle cell differentiation and disease risk
Relations
Reanalysis of GSM1246721
BioProject PRJNA474527
SRA SRP149730

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE115317_RAW.tar 368.4 Mb (http)(custom) TAR (of BW, NARROWPEAK)
GSE115317_reanalyzed_SMAD3_A549.bw 208.8 Mb (ftp)(http) BW
GSE115317_reanalyzed_SMAD3_A549_peaks.narrowPeak.gz 614.1 Kb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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