Characterization of TCF21 Downstream Target Regions Identifies a Transcriptional Network Linking Multiple Independent Coronary Artery Disease Loci

Abstract

To functionally link coronary artery disease (CAD) causal genes identified by genome wide association studies (GWAS), and to investigate the cellular and molecular mechanisms of atherosclerosis, we have used chromatin immunoprecipitation sequencing (ChIP-Seq) with the CAD associated transcription factor TCF21 in human coronary artery smooth muscle cells (HCASMC). Analysis of identified TCF21 target genes for enrichment of molecular and cellular annotation terms identified processes relevant to CAD pathophysiology, including “growth factor binding,” “matrix interaction,” and “smooth muscle contraction.” We characterized the canonical binding sequence for TCF21 as CAGCTG, identified AP-1 binding sites in TCF21 peaks, and by conducting ChIP-Seq for JUN and JUND in HCASMC confirmed that there is significant overlap between TCF21 and AP-1 binding loci in this cell type. Expression quantitative trait variation mapped to target genes of TCF21 was significantly enriched among variants with low P-values in the GWAS analyses, suggesting a possible functional interaction between TCF21 binding and causal variants in other CAD disease loci. Separate enrichment analyses found over-representation of TCF21 target genes among CAD associated genes, and linkage disequilibrium between TCF21 peak variation and that found in GWAS loci, consistent with the hypothesis that TCF21 may affect disease risk through interaction with other disease associated loci. Interestingly, enrichment for TCF21 target genes was also found among other genome wide association phenotypes, including height and inflammatory bowel disease, suggesting a functional profile important for basic cellular processes in non-vascular tissues. Thus, data and analyses presented here suggest that study of GWAS transcription factors may be a highly useful approach to identifying disease gene interactions and thus pathways that may be relevant to complex disease etiology.

Genetics of Coronary Artery Disease

“…In further studies in the mouse, genetically increased hepatic sortilin expression was shown to both reduce hepatic APOB secretion and increase LDL catabolism, providing dual mechanisms for the strong association between increased hepatic sortilin-1 expression and reduced plasma LDL-C levels in humans. 138 In another recent investigation of GWAS significant loci, Sazonova et al 139 used a complex series of bioinformatic, molecular, cell biology, and system genetic approaches to show that the transcription factor, TCF21, regulates a transcriptional network linking multiple independent CAD loci. The same group demonstrated that TCF21 regulates the development of the epicardial progenitor cells that give risk to smooth muscle cells that contribute to the fibrous cap.…”

Transcriptional control of cardiac fibroblast plasticity

“…Animals deficient in Tcf21 fail to produce CFs, instead accumulating cells expressing SMC markers on the surface of the heart [58, 59]. RNA-sequencing of Tcf21 -deficient coronary SMC combined with Ingenuity Pathway Analysis revealed that TCF21 promotes a gene expression signature consistent with cell proliferation and migration while inhibiting SMC differentiation [60]. ChIP-sequencing identified 5' – CAGCTG – 3' as the canonical binding sequence for TCF21 and suggests shared genomic occupancy with other transcription factors, including AP-1, TEAD, C/EBP, and ATF.…”

ChIP-seq in Studying Epigenetic Mechanisms of Disease and Promoting Precision Medicine: Progresses and Future Directions

“…Some transcription factors are well-known players in cancer, such as androgen receptor in prostate cancer [35] and estrogen receptor-α in breast cancer [23]. Recent studies also revealed the involvement of transcription factors in noncancerous diseases [11,[39][40].…”

“…In addition, ChIP-seq revealed the roles for several transcription factors in cardiovascular disease [11,40] and neurodegenerative disease [60]. For example, the gene encoding TCF21 is associated with coronary artery disease [11]; TCF21 preferentially targeted genes that are also linked to this disease.…”

“…For example, the gene encoding TCF21 is associated with coronary artery disease [11]; TCF21 preferentially targeted genes that are also linked to this disease. These studies illustrated the power of ChIP-seq in revealing epigenetic abnormalities in disease.…”