The Experts below are selected from a list of 28917 Experts worldwide ranked by ideXlab platform
Thomas Quertermous - One of the best experts on this subject based on the ideXlab platform.
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coronary disease associated gene TCF21 inhibits smooth muscle cell differentiation by blocking the myocardin serum response factor pathway
Circulation Research, 2020Co-Authors: Manabu Nagao, Milos Pjanic, Trieu Nguyen, Quanyi Zhao, Paul Cheng, Robert C Wirka, Joetsaroop Bagga, Joseph M Miano, Thomas QuertermousAbstract:Rationale: The gene encoding transcription factor TCF21 has been linked to coronary artery disease (CAD) risk by human genome wide association studies (GWAS) in multiple racial ethnic groups. In mu...
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coronary disease associated gene TCF21 inhibits smooth muscle cell differentiation by blocking the myocardin serum response factor pathway
Circulation Research, 2020Co-Authors: Manabu Nagao, Milos Pjanic, Trieu Nguyen, Quanyi Zhao, Paul Cheng, Robert C Wirka, Joseph M Miano, Joetsaroop S Bagga, Thomas QuertermousAbstract:Rationale: The gene encoding TCF21 (transcription factor 21) has been linked to coronary artery disease risk by human genome-wide association studies in multiple racial ethnic groups. In murine mod...
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lncrna de novo discovery reveals noncoding rnas as major molecular mechanism associating coronary artery disease gwas variants with causal genes to confer disease risk
bioRxiv, 2019Co-Authors: Milos Pjanic, Clint L. Miller, Juyong Brian Kim, Trieu Nguyen, Quanyi Zhao, Paul Cheng, Robert C Wirka, Thomas QuertermousAbstract:Long noncoding RNAs (lncRNA) comprise an underlying regulatory network in the human genome that remains largely unexplored and could represent a molecular mechanism connecting GWAS risk variants with the disease causal genes. Human coronary artery smooth muscle cells (HCASMC) are one of the most important cells in the regulation of atherosclerotic disease progression. In this study, we aimed to discover the HCASMC-specific lncRNA collection and to explore the mechanistic relationship between HCAMSC lncRNAs with increased disease risk for coronary artery disease. We applied 6 different stimuli relevant to athero-condition, including stimulations with TGFbeta, TNFalpha, PDGFD and serum, and two transcription factor knock-downs TCF21 and SMAD3, and performed deep RNA sequencing on 48 HCASMC samples. We designed a lncRNA discovery pipeline to maximize the detection of tissue specific and low expressed lncRNAs. This generated a set of 53076 lncRNAs, that showed increased association with CAD GWAS variants, various HCASMC eQTL data sets and GTEx eQTLs for tissues enriched in smooth muscle. Module analysis revealed lncRNAs highly associated with TGFbeta and general pro-differentiation traits located in the CAD GWAS loci, such as, FES/FURIN, COL4A1/A2, CDKN2A/B, TGFB1, and FN1. Transcription factor motif analysis revealed the presence of HCASMC relevant factors, such as, TCF21, ZEB1, ZEB2, JUN, JUND, and an SRF cofactor ELK4, near the boundaries of HCASMC lncRNA. We defined lncRNA QTLs using the GTEx Coronary Artery dataset, and showed colocalization with other HCASMC QTLs, such as expression QTLs, chromatin looping QTLs, chromatin accessibility QTLs and TCF21 binding QTLs. We show several examples of CAD GWAS loci where lncRNAs show regulatory function, such as FES/FURIN, FN1, COL4A1/A2 and TGFB1. We unraveled a complex network of regulatory interactions at FES/FURIN locus, involving TCF21 and lncRNA 43779.9, and present a model in which TCF21 inhibited lncRNA 43779.9 regulates FES gene and indirectly the pro-differentiation FURIN gene by creating a looping interaction with the intron 1 of FES transcript. We define 5 regulatory variants at the FES/FURIN locus and propose a causal variant, rs35346340, that disrupts TCF21 binding and subsequently influences 43779.9 expression. Finally, we show the presence of lncRNAs in deeply sequenced TCF21 pooled ChIPSeq and discover TCF21 binding lncRNAs, 3938.1 and 3852.1 as ACTA2-regulating transcripts. This study defines lncRNAs as essential regulators of GWAS loci and shows the importance of using deep sequencing approach to further explore the genomic regulatory landscape of lncRNAs in human tissues.
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TCF21 and ap 1 interact through epigenetic modifications to regulate coronary artery disease gene expression
Genome Medicine, 2019Co-Authors: Quanyi Zhao, Milos Pjanic, Clint L. Miller, Juyong Brian Kim, Trieu Nguyen, Manabu Nagao, Paul Cheng, Robert C Wirka, Thomas QuertermousAbstract:Genome-wide association studies have identified over 160 loci that are associated with coronary artery disease. As with other complex human diseases, risk in coronary disease loci is determined primarily by altered expression of the causal gene, due to variation in binding of transcription factors and chromatin-modifying proteins that directly regulate the transcriptional apparatus. We have previously identified a coronary disease network downstream of the disease-associated transcription factor TCF21, and in work reported here extends these studies to investigate the mechanisms by which it interacts with the AP-1 transcription complex to regulate local epigenetic effects in these downstream coronary disease loci. Genomic studies, including chromatin immunoprecipitation sequencing, RNA sequencing, and protein-protein interaction studies, were performed in human coronary artery smooth muscle cells. We show here that TCF21 and JUN regulate expression of two presumptive causal coronary disease genes, SMAD3 and CDKN2B-AS1, in part by interactions with histone deacetylases and acetyltransferases. Genome-wide TCF21 and JUN binding is jointly localized and particularly enriched in coronary disease loci where they broadly modulate H3K27Ac and chromatin state changes linked to disease-related processes in vascular cells. Heterozygosity at coronary disease causal variation, or genome editing of these variants, is associated with decreased binding of both JUN and TCF21 and loss of expression in cis, supporting a transcriptional mechanism for disease risk. These data show that the known chromatin remodeling and pioneer functions of AP-1 are a pervasive aspect of epigenetic control of transcription, and thus, the risk in coronary disease-associated loci, and that interaction of AP-1 with TCF21 to control epigenetic features, contributes to the genetic risk in loci where they co-localize.
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abstract 18374 TCF21 and aryl hydrocarbon receptor gene cooperate to activate a pro atherosclerotic gene expression program
Circulation, 2016Co-Authors: Juyong Brian Kim, Milos Pjanic, Clint L. Miller, Olga Sazanova, Tina Wang, Trieu Nguyen, Lars Maegdefessel, Ulf Hedin, Thomas QuertermousAbstract:Background: Recently, the TCF21 gene was linked to the highly replicated coronary artery disease (CAD) associated polymorphism in the 6q23 locus. We previously reported Aryl Hydrocarbon Receptor ( AHR ) to be a downstream target of TCF21. AHR is a ligand-activated transcription factor that mediates the cellular response to environmental contaminants, including dioxin and polycyclic aromatic hydrocarbons (e.g. cigarette), and has recently been associated with CAD in mice and humans. We further characterized the interaction between TCF21 and AHR. Methods: The co-regulatory role of TCF21 and AHR on transcription was tested using dual luciferase assay. Luciferase reporter vector containing TCF21 and AHR binding motifs were transfected into HEK293 cells, with or without TCF21 expressing plasmid. These cells were then treated with 2,3,7,8-Tetrachlorodibenxo- p -dioxin (TCDD) or control. Laser capture microdissection (LCM) was performed on atherosclerotic plaque of Apoe (-/-) mouse on high fat diet for 12 weeks. Previously performed ChIP-Seq and ATAC-Seq (Assay for Transposase-Accessible Chromatin using sequencing) data from human coronary artery smooth muscle cells (HCASMC) were analyzed. Position weight matrix for TCF21 and AHR were obtained from the JASPAR database. Results: We found that TCF21 over-expression and AHR pathway activation additively increased downstream transcription using reporter assay. Furthermore, we found AHR level to be higher in plaque in human and mouse atherosclerotic plaques. The TCF21 and AHR binding sites co-localized genome-wide to open chromatin regions of HCASMC, and genes near the overlapped binding sites enriched for pathways relevant to atherosclerosis, including cytokine production, migration and ossification. Using published ChIP-Seq data, we also found that common peaks of AHR-ARNT and TCF21 ChIP-Seq enriched for GWAS SNPs related to coronary artery disease. Conclusion: The binding sites of two TFs , TCF21 and AHR , co-localize in HCASMC, and cooperate in transcriptional activation of downstream genes relevant to atherosclerosis. The functional link between TCF21 and AHR provides an opportunity to explore gene by environment interactions in the pathogenesis of CAD.
Clint L. Miller - One of the best experts on this subject based on the ideXlab platform.
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lncrna de novo discovery reveals noncoding rnas as major molecular mechanism associating coronary artery disease gwas variants with causal genes to confer disease risk
bioRxiv, 2019Co-Authors: Milos Pjanic, Clint L. Miller, Juyong Brian Kim, Trieu Nguyen, Quanyi Zhao, Paul Cheng, Robert C Wirka, Thomas QuertermousAbstract:Long noncoding RNAs (lncRNA) comprise an underlying regulatory network in the human genome that remains largely unexplored and could represent a molecular mechanism connecting GWAS risk variants with the disease causal genes. Human coronary artery smooth muscle cells (HCASMC) are one of the most important cells in the regulation of atherosclerotic disease progression. In this study, we aimed to discover the HCASMC-specific lncRNA collection and to explore the mechanistic relationship between HCAMSC lncRNAs with increased disease risk for coronary artery disease. We applied 6 different stimuli relevant to athero-condition, including stimulations with TGFbeta, TNFalpha, PDGFD and serum, and two transcription factor knock-downs TCF21 and SMAD3, and performed deep RNA sequencing on 48 HCASMC samples. We designed a lncRNA discovery pipeline to maximize the detection of tissue specific and low expressed lncRNAs. This generated a set of 53076 lncRNAs, that showed increased association with CAD GWAS variants, various HCASMC eQTL data sets and GTEx eQTLs for tissues enriched in smooth muscle. Module analysis revealed lncRNAs highly associated with TGFbeta and general pro-differentiation traits located in the CAD GWAS loci, such as, FES/FURIN, COL4A1/A2, CDKN2A/B, TGFB1, and FN1. Transcription factor motif analysis revealed the presence of HCASMC relevant factors, such as, TCF21, ZEB1, ZEB2, JUN, JUND, and an SRF cofactor ELK4, near the boundaries of HCASMC lncRNA. We defined lncRNA QTLs using the GTEx Coronary Artery dataset, and showed colocalization with other HCASMC QTLs, such as expression QTLs, chromatin looping QTLs, chromatin accessibility QTLs and TCF21 binding QTLs. We show several examples of CAD GWAS loci where lncRNAs show regulatory function, such as FES/FURIN, FN1, COL4A1/A2 and TGFB1. We unraveled a complex network of regulatory interactions at FES/FURIN locus, involving TCF21 and lncRNA 43779.9, and present a model in which TCF21 inhibited lncRNA 43779.9 regulates FES gene and indirectly the pro-differentiation FURIN gene by creating a looping interaction with the intron 1 of FES transcript. We define 5 regulatory variants at the FES/FURIN locus and propose a causal variant, rs35346340, that disrupts TCF21 binding and subsequently influences 43779.9 expression. Finally, we show the presence of lncRNAs in deeply sequenced TCF21 pooled ChIPSeq and discover TCF21 binding lncRNAs, 3938.1 and 3852.1 as ACTA2-regulating transcripts. This study defines lncRNAs as essential regulators of GWAS loci and shows the importance of using deep sequencing approach to further explore the genomic regulatory landscape of lncRNAs in human tissues.
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atheroprotective roles of smooth muscle cell phenotypic modulation and the TCF21 disease gene as revealed by single cell analysis
Nature Medicine, 2019Co-Authors: Milos Pjanic, Trieu Nguyen, Robert C Wirka, Dhananjay Wagh, David T Paik, Clint L. MillerAbstract:In response to various stimuli, vascular smooth muscle cells (SMCs) can de-differentiate, proliferate and migrate in a process known as phenotypic modulation. However, the phenotype of modulated SMCs in vivo during atherosclerosis and the influence of this process on coronary artery disease (CAD) risk have not been clearly established. Using single-cell RNA sequencing, we comprehensively characterized the transcriptomic phenotype of modulated SMCs in vivo in atherosclerotic lesions of both mouse and human arteries and found that these cells transform into unique fibroblast-like cells, termed 'fibromyocytes', rather than into a classical macrophage phenotype. SMC-specific knockout of TCF21-a causal CAD gene-markedly inhibited SMC phenotypic modulation in mice, leading to the presence of fewer fibromyocytes within lesions as well as within the protective fibrous cap of the lesions. Moreover, TCF21 expression was strongly associated with SMC phenotypic modulation in diseased human coronary arteries, and higher levels of TCF21 expression were associated with decreased CAD risk in human CAD-relevant tissues. These results establish a protective role for both TCF21 and SMC phenotypic modulation in this disease.
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TCF21 and ap 1 interact through epigenetic modifications to regulate coronary artery disease gene expression
Genome Medicine, 2019Co-Authors: Quanyi Zhao, Milos Pjanic, Clint L. Miller, Juyong Brian Kim, Trieu Nguyen, Manabu Nagao, Paul Cheng, Robert C Wirka, Thomas QuertermousAbstract:Genome-wide association studies have identified over 160 loci that are associated with coronary artery disease. As with other complex human diseases, risk in coronary disease loci is determined primarily by altered expression of the causal gene, due to variation in binding of transcription factors and chromatin-modifying proteins that directly regulate the transcriptional apparatus. We have previously identified a coronary disease network downstream of the disease-associated transcription factor TCF21, and in work reported here extends these studies to investigate the mechanisms by which it interacts with the AP-1 transcription complex to regulate local epigenetic effects in these downstream coronary disease loci. Genomic studies, including chromatin immunoprecipitation sequencing, RNA sequencing, and protein-protein interaction studies, were performed in human coronary artery smooth muscle cells. We show here that TCF21 and JUN regulate expression of two presumptive causal coronary disease genes, SMAD3 and CDKN2B-AS1, in part by interactions with histone deacetylases and acetyltransferases. Genome-wide TCF21 and JUN binding is jointly localized and particularly enriched in coronary disease loci where they broadly modulate H3K27Ac and chromatin state changes linked to disease-related processes in vascular cells. Heterozygosity at coronary disease causal variation, or genome editing of these variants, is associated with decreased binding of both JUN and TCF21 and loss of expression in cis, supporting a transcriptional mechanism for disease risk. These data show that the known chromatin remodeling and pioneer functions of AP-1 are a pervasive aspect of epigenetic control of transcription, and thus, the risk in coronary disease-associated loci, and that interaction of AP-1 with TCF21 to control epigenetic features, contributes to the genetic risk in loci where they co-localize.
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coronary artery disease genes smad3 and TCF21 promote opposing interactive genetic programs that regulate smooth muscle cell differentiation and disease risk
PLOS Genetics, 2018Co-Authors: Dharini Iyer, Clint L. Miller, Trieu Nguyen, Quanyi Zhao, Ameay Naravane, Boxiang Liu, Manabu Nagao, Paul Cheng, Robert C Wirka, Juyong Brian KimAbstract:Although numerous genetic loci have been associated with coronary artery disease (CAD) with genome wide association studies, efforts are needed to identify the causal genes in these loci and link them into fundamental signaling pathways. Recent studies have investigated the disease mechanism of CAD associated gene SMAD3, a central transcription factor (TF) in the TGFβ pathway, investigating its role in smooth muscle biology. In vitro studies in human coronary artery smooth muscle cells (HCASMC) revealed that SMAD3 modulates cellular phenotype, promoting expression of differentiation marker genes while inhibiting proliferation. RNA sequencing and chromatin immunoprecipitation sequencing studies in HCASMC identified downstream genes that reside in pathways which mediate vascular development and atherosclerosis processes in this cell type. HCASMC phenotype, and gene expression patterns promoted by SMAD3 were noted to have opposing direction of effect compared to another CAD associated TF, TCF21. At sites of SMAD3 and TCF21 colocalization on DNA, SMAD3 binding was inversely correlated with TCF21 binding, due in part to TCF21 locally blocking chromatin accessibility at the SMAD3 binding site. Further, TCF21 was able to directly inhibit SMAD3 activation of gene expression in transfection reporter gene studies. In contrast to TCF21 which is protective toward CAD, SMAD3 expression in HCASMC was shown to be directly correlated with disease risk. We propose that the pro-differentiation action of SMAD3 inhibits dedifferentiation that is required for HCASMC to expand and stabilize disease plaque as they respond to vascular stresses, counteracting the protective dedifferentiating activity of TCF21 and promoting disease risk.
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SMAD3 and TCF21 have opposing binding behavior and transcriptional regulatory functions in HCASMC.
2018Co-Authors: Dharini Iyer, Clint L. Miller, Trieu Nguyen, Quanyi Zhao, Robert Wirka, Ameay Naravane, Boxiang Liu, Manabu Nagao, Paul Cheng, Juyong Brian KimAbstract:A) SMAD3 and TCF21 joint binding regions were analyzed for degree occupancy by each factor. DNA occupancy was assessed by comparing peak reads normalized to background reads and this variable graphed. More than half of the colocalized binding regions were biased for either SMAD3 or TCF21 binding, with a 2-fold greater number of normalized reads for one or the other factor. B) To serve as a control for SMAD3 and TCF21 binding patterns, we characterized binding of AP1 heterodimer transcription factors JUN and JUND. Compared to the SMAD3 and TCF21 pattern, there is equivalent binding at the majority of AP1 target sites in the genome. C) SMAD3 binding at the SERPINE1 and COL1A1 loci where it colocalizes with TCF21 was assessed by ChIP-PCR in HCASMC. Knockdown of TCF21 mRNA levels by specific siRNA was associated with increased binding of SMAD3 compared to cells transfected with scrambled siRNA (SCR). D) Local chromatin accessibility was evaluated at the SERPINE1 and COL1A1 loci with the assay for transposase-accessible chromatin coupled with quantitative PCR (ATAC-PCR), in HCASMC with knockdown by siTCF21. E) Reporter gene transfection studies evaluated relative transcriptional activity of SMAD3 and TCF21 at a SERPINE1 enhancer region, in an established human umbilical vein smooth muscle cell line (HUVSMC). F) Identical experiments were conducted in primary cultured HCASMC.
Milos Pjanic - One of the best experts on this subject based on the ideXlab platform.
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coronary disease associated gene TCF21 inhibits smooth muscle cell differentiation by blocking the myocardin serum response factor pathway
Circulation Research, 2020Co-Authors: Manabu Nagao, Milos Pjanic, Trieu Nguyen, Quanyi Zhao, Paul Cheng, Robert C Wirka, Joetsaroop Bagga, Joseph M Miano, Thomas QuertermousAbstract:Rationale: The gene encoding transcription factor TCF21 has been linked to coronary artery disease (CAD) risk by human genome wide association studies (GWAS) in multiple racial ethnic groups. In mu...
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coronary disease associated gene TCF21 inhibits smooth muscle cell differentiation by blocking the myocardin serum response factor pathway
Circulation Research, 2020Co-Authors: Manabu Nagao, Milos Pjanic, Trieu Nguyen, Quanyi Zhao, Paul Cheng, Robert C Wirka, Joseph M Miano, Joetsaroop S Bagga, Thomas QuertermousAbstract:Rationale: The gene encoding TCF21 (transcription factor 21) has been linked to coronary artery disease risk by human genome-wide association studies in multiple racial ethnic groups. In murine mod...
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lncrna de novo discovery reveals noncoding rnas as major molecular mechanism associating coronary artery disease gwas variants with causal genes to confer disease risk
bioRxiv, 2019Co-Authors: Milos Pjanic, Clint L. Miller, Juyong Brian Kim, Trieu Nguyen, Quanyi Zhao, Paul Cheng, Robert C Wirka, Thomas QuertermousAbstract:Long noncoding RNAs (lncRNA) comprise an underlying regulatory network in the human genome that remains largely unexplored and could represent a molecular mechanism connecting GWAS risk variants with the disease causal genes. Human coronary artery smooth muscle cells (HCASMC) are one of the most important cells in the regulation of atherosclerotic disease progression. In this study, we aimed to discover the HCASMC-specific lncRNA collection and to explore the mechanistic relationship between HCAMSC lncRNAs with increased disease risk for coronary artery disease. We applied 6 different stimuli relevant to athero-condition, including stimulations with TGFbeta, TNFalpha, PDGFD and serum, and two transcription factor knock-downs TCF21 and SMAD3, and performed deep RNA sequencing on 48 HCASMC samples. We designed a lncRNA discovery pipeline to maximize the detection of tissue specific and low expressed lncRNAs. This generated a set of 53076 lncRNAs, that showed increased association with CAD GWAS variants, various HCASMC eQTL data sets and GTEx eQTLs for tissues enriched in smooth muscle. Module analysis revealed lncRNAs highly associated with TGFbeta and general pro-differentiation traits located in the CAD GWAS loci, such as, FES/FURIN, COL4A1/A2, CDKN2A/B, TGFB1, and FN1. Transcription factor motif analysis revealed the presence of HCASMC relevant factors, such as, TCF21, ZEB1, ZEB2, JUN, JUND, and an SRF cofactor ELK4, near the boundaries of HCASMC lncRNA. We defined lncRNA QTLs using the GTEx Coronary Artery dataset, and showed colocalization with other HCASMC QTLs, such as expression QTLs, chromatin looping QTLs, chromatin accessibility QTLs and TCF21 binding QTLs. We show several examples of CAD GWAS loci where lncRNAs show regulatory function, such as FES/FURIN, FN1, COL4A1/A2 and TGFB1. We unraveled a complex network of regulatory interactions at FES/FURIN locus, involving TCF21 and lncRNA 43779.9, and present a model in which TCF21 inhibited lncRNA 43779.9 regulates FES gene and indirectly the pro-differentiation FURIN gene by creating a looping interaction with the intron 1 of FES transcript. We define 5 regulatory variants at the FES/FURIN locus and propose a causal variant, rs35346340, that disrupts TCF21 binding and subsequently influences 43779.9 expression. Finally, we show the presence of lncRNAs in deeply sequenced TCF21 pooled ChIPSeq and discover TCF21 binding lncRNAs, 3938.1 and 3852.1 as ACTA2-regulating transcripts. This study defines lncRNAs as essential regulators of GWAS loci and shows the importance of using deep sequencing approach to further explore the genomic regulatory landscape of lncRNAs in human tissues.
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atheroprotective roles of smooth muscle cell phenotypic modulation and the TCF21 disease gene as revealed by single cell analysis
Nature Medicine, 2019Co-Authors: Milos Pjanic, Trieu Nguyen, Robert C Wirka, Dhananjay Wagh, David T Paik, Clint L. MillerAbstract:In response to various stimuli, vascular smooth muscle cells (SMCs) can de-differentiate, proliferate and migrate in a process known as phenotypic modulation. However, the phenotype of modulated SMCs in vivo during atherosclerosis and the influence of this process on coronary artery disease (CAD) risk have not been clearly established. Using single-cell RNA sequencing, we comprehensively characterized the transcriptomic phenotype of modulated SMCs in vivo in atherosclerotic lesions of both mouse and human arteries and found that these cells transform into unique fibroblast-like cells, termed 'fibromyocytes', rather than into a classical macrophage phenotype. SMC-specific knockout of TCF21-a causal CAD gene-markedly inhibited SMC phenotypic modulation in mice, leading to the presence of fewer fibromyocytes within lesions as well as within the protective fibrous cap of the lesions. Moreover, TCF21 expression was strongly associated with SMC phenotypic modulation in diseased human coronary arteries, and higher levels of TCF21 expression were associated with decreased CAD risk in human CAD-relevant tissues. These results establish a protective role for both TCF21 and SMC phenotypic modulation in this disease.
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TCF21 and ap 1 interact through epigenetic modifications to regulate coronary artery disease gene expression
Genome Medicine, 2019Co-Authors: Quanyi Zhao, Milos Pjanic, Clint L. Miller, Juyong Brian Kim, Trieu Nguyen, Manabu Nagao, Paul Cheng, Robert C Wirka, Thomas QuertermousAbstract:Genome-wide association studies have identified over 160 loci that are associated with coronary artery disease. As with other complex human diseases, risk in coronary disease loci is determined primarily by altered expression of the causal gene, due to variation in binding of transcription factors and chromatin-modifying proteins that directly regulate the transcriptional apparatus. We have previously identified a coronary disease network downstream of the disease-associated transcription factor TCF21, and in work reported here extends these studies to investigate the mechanisms by which it interacts with the AP-1 transcription complex to regulate local epigenetic effects in these downstream coronary disease loci. Genomic studies, including chromatin immunoprecipitation sequencing, RNA sequencing, and protein-protein interaction studies, were performed in human coronary artery smooth muscle cells. We show here that TCF21 and JUN regulate expression of two presumptive causal coronary disease genes, SMAD3 and CDKN2B-AS1, in part by interactions with histone deacetylases and acetyltransferases. Genome-wide TCF21 and JUN binding is jointly localized and particularly enriched in coronary disease loci where they broadly modulate H3K27Ac and chromatin state changes linked to disease-related processes in vascular cells. Heterozygosity at coronary disease causal variation, or genome editing of these variants, is associated with decreased binding of both JUN and TCF21 and loss of expression in cis, supporting a transcriptional mechanism for disease risk. These data show that the known chromatin remodeling and pioneer functions of AP-1 are a pervasive aspect of epigenetic control of transcription, and thus, the risk in coronary disease-associated loci, and that interaction of AP-1 with TCF21 to control epigenetic features, contributes to the genetic risk in loci where they co-localize.
Juyong Brian Kim - One of the best experts on this subject based on the ideXlab platform.
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lncrna de novo discovery reveals noncoding rnas as major molecular mechanism associating coronary artery disease gwas variants with causal genes to confer disease risk
bioRxiv, 2019Co-Authors: Milos Pjanic, Clint L. Miller, Juyong Brian Kim, Trieu Nguyen, Quanyi Zhao, Paul Cheng, Robert C Wirka, Thomas QuertermousAbstract:Long noncoding RNAs (lncRNA) comprise an underlying regulatory network in the human genome that remains largely unexplored and could represent a molecular mechanism connecting GWAS risk variants with the disease causal genes. Human coronary artery smooth muscle cells (HCASMC) are one of the most important cells in the regulation of atherosclerotic disease progression. In this study, we aimed to discover the HCASMC-specific lncRNA collection and to explore the mechanistic relationship between HCAMSC lncRNAs with increased disease risk for coronary artery disease. We applied 6 different stimuli relevant to athero-condition, including stimulations with TGFbeta, TNFalpha, PDGFD and serum, and two transcription factor knock-downs TCF21 and SMAD3, and performed deep RNA sequencing on 48 HCASMC samples. We designed a lncRNA discovery pipeline to maximize the detection of tissue specific and low expressed lncRNAs. This generated a set of 53076 lncRNAs, that showed increased association with CAD GWAS variants, various HCASMC eQTL data sets and GTEx eQTLs for tissues enriched in smooth muscle. Module analysis revealed lncRNAs highly associated with TGFbeta and general pro-differentiation traits located in the CAD GWAS loci, such as, FES/FURIN, COL4A1/A2, CDKN2A/B, TGFB1, and FN1. Transcription factor motif analysis revealed the presence of HCASMC relevant factors, such as, TCF21, ZEB1, ZEB2, JUN, JUND, and an SRF cofactor ELK4, near the boundaries of HCASMC lncRNA. We defined lncRNA QTLs using the GTEx Coronary Artery dataset, and showed colocalization with other HCASMC QTLs, such as expression QTLs, chromatin looping QTLs, chromatin accessibility QTLs and TCF21 binding QTLs. We show several examples of CAD GWAS loci where lncRNAs show regulatory function, such as FES/FURIN, FN1, COL4A1/A2 and TGFB1. We unraveled a complex network of regulatory interactions at FES/FURIN locus, involving TCF21 and lncRNA 43779.9, and present a model in which TCF21 inhibited lncRNA 43779.9 regulates FES gene and indirectly the pro-differentiation FURIN gene by creating a looping interaction with the intron 1 of FES transcript. We define 5 regulatory variants at the FES/FURIN locus and propose a causal variant, rs35346340, that disrupts TCF21 binding and subsequently influences 43779.9 expression. Finally, we show the presence of lncRNAs in deeply sequenced TCF21 pooled ChIPSeq and discover TCF21 binding lncRNAs, 3938.1 and 3852.1 as ACTA2-regulating transcripts. This study defines lncRNAs as essential regulators of GWAS loci and shows the importance of using deep sequencing approach to further explore the genomic regulatory landscape of lncRNAs in human tissues.
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TCF21 and ap 1 interact through epigenetic modifications to regulate coronary artery disease gene expression
Genome Medicine, 2019Co-Authors: Quanyi Zhao, Milos Pjanic, Clint L. Miller, Juyong Brian Kim, Trieu Nguyen, Manabu Nagao, Paul Cheng, Robert C Wirka, Thomas QuertermousAbstract:Genome-wide association studies have identified over 160 loci that are associated with coronary artery disease. As with other complex human diseases, risk in coronary disease loci is determined primarily by altered expression of the causal gene, due to variation in binding of transcription factors and chromatin-modifying proteins that directly regulate the transcriptional apparatus. We have previously identified a coronary disease network downstream of the disease-associated transcription factor TCF21, and in work reported here extends these studies to investigate the mechanisms by which it interacts with the AP-1 transcription complex to regulate local epigenetic effects in these downstream coronary disease loci. Genomic studies, including chromatin immunoprecipitation sequencing, RNA sequencing, and protein-protein interaction studies, were performed in human coronary artery smooth muscle cells. We show here that TCF21 and JUN regulate expression of two presumptive causal coronary disease genes, SMAD3 and CDKN2B-AS1, in part by interactions with histone deacetylases and acetyltransferases. Genome-wide TCF21 and JUN binding is jointly localized and particularly enriched in coronary disease loci where they broadly modulate H3K27Ac and chromatin state changes linked to disease-related processes in vascular cells. Heterozygosity at coronary disease causal variation, or genome editing of these variants, is associated with decreased binding of both JUN and TCF21 and loss of expression in cis, supporting a transcriptional mechanism for disease risk. These data show that the known chromatin remodeling and pioneer functions of AP-1 are a pervasive aspect of epigenetic control of transcription, and thus, the risk in coronary disease-associated loci, and that interaction of AP-1 with TCF21 to control epigenetic features, contributes to the genetic risk in loci where they co-localize.
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coronary artery disease genes smad3 and TCF21 promote opposing interactive genetic programs that regulate smooth muscle cell differentiation and disease risk
PLOS Genetics, 2018Co-Authors: Dharini Iyer, Clint L. Miller, Trieu Nguyen, Quanyi Zhao, Ameay Naravane, Boxiang Liu, Manabu Nagao, Paul Cheng, Robert C Wirka, Juyong Brian KimAbstract:Although numerous genetic loci have been associated with coronary artery disease (CAD) with genome wide association studies, efforts are needed to identify the causal genes in these loci and link them into fundamental signaling pathways. Recent studies have investigated the disease mechanism of CAD associated gene SMAD3, a central transcription factor (TF) in the TGFβ pathway, investigating its role in smooth muscle biology. In vitro studies in human coronary artery smooth muscle cells (HCASMC) revealed that SMAD3 modulates cellular phenotype, promoting expression of differentiation marker genes while inhibiting proliferation. RNA sequencing and chromatin immunoprecipitation sequencing studies in HCASMC identified downstream genes that reside in pathways which mediate vascular development and atherosclerosis processes in this cell type. HCASMC phenotype, and gene expression patterns promoted by SMAD3 were noted to have opposing direction of effect compared to another CAD associated TF, TCF21. At sites of SMAD3 and TCF21 colocalization on DNA, SMAD3 binding was inversely correlated with TCF21 binding, due in part to TCF21 locally blocking chromatin accessibility at the SMAD3 binding site. Further, TCF21 was able to directly inhibit SMAD3 activation of gene expression in transfection reporter gene studies. In contrast to TCF21 which is protective toward CAD, SMAD3 expression in HCASMC was shown to be directly correlated with disease risk. We propose that the pro-differentiation action of SMAD3 inhibits dedifferentiation that is required for HCASMC to expand and stabilize disease plaque as they respond to vascular stresses, counteracting the protective dedifferentiating activity of TCF21 and promoting disease risk.
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SMAD3 and TCF21 have opposing binding behavior and transcriptional regulatory functions in HCASMC.
2018Co-Authors: Dharini Iyer, Clint L. Miller, Trieu Nguyen, Quanyi Zhao, Robert Wirka, Ameay Naravane, Boxiang Liu, Manabu Nagao, Paul Cheng, Juyong Brian KimAbstract:A) SMAD3 and TCF21 joint binding regions were analyzed for degree occupancy by each factor. DNA occupancy was assessed by comparing peak reads normalized to background reads and this variable graphed. More than half of the colocalized binding regions were biased for either SMAD3 or TCF21 binding, with a 2-fold greater number of normalized reads for one or the other factor. B) To serve as a control for SMAD3 and TCF21 binding patterns, we characterized binding of AP1 heterodimer transcription factors JUN and JUND. Compared to the SMAD3 and TCF21 pattern, there is equivalent binding at the majority of AP1 target sites in the genome. C) SMAD3 binding at the SERPINE1 and COL1A1 loci where it colocalizes with TCF21 was assessed by ChIP-PCR in HCASMC. Knockdown of TCF21 mRNA levels by specific siRNA was associated with increased binding of SMAD3 compared to cells transfected with scrambled siRNA (SCR). D) Local chromatin accessibility was evaluated at the SERPINE1 and COL1A1 loci with the assay for transposase-accessible chromatin coupled with quantitative PCR (ATAC-PCR), in HCASMC with knockdown by siTCF21. E) Reporter gene transfection studies evaluated relative transcriptional activity of SMAD3 and TCF21 at a SERPINE1 enhancer region, in an established human umbilical vein smooth muscle cell line (HUVSMC). F) Identical experiments were conducted in primary cultured HCASMC.
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AHR expression in HCASMC is mediated by an eQTL that modulates TCF21 binding.
2017Co-Authors: Juyong Brian Kim, Milos Pjanic, Ting Wang, Clint L. Miller, Trieu Nguyen, Dharini Iyer, Boxiang Liu, Olga Sazonova, Ivan Carcamo-orive, Ljubica Perisic MaticAbstract:(a) The downstream region of the AHR gene on chr7 (located on >20kb distance from the transcription end site) contains a strong open chromatin region and enhancer in HCASMC marked by ATAC-Seq, H3K27ac tracks and binding of AP1 transcription factors, JUN and JUND, as well as TCF21. Enhanced view shows that SNP rs10265174 directly overlaps the ATAC-Seq open chromatin, H3K27ac enhancer mark, JUN and JUND ChIP-Seq peaks, and is within a broad TCF21 ChIP-Seq peak. (b) The LocusZoom plot shows AHR gene eQTL distribution in HCASMC across 1Mb (16.9–17.9Mb) on chr7 encompassing AHR gene, with SNP rs10265174 being the top eQTL in the locus. (c) rs10265174 alters the position weight matrix scores for AP1 and TCF4 transcription factors (data from Haploreg). (d) TCF21 ChIP-qPCR shows enrichment at the AHR upstream genomic region compared to IgG control (p
Trieu Nguyen - One of the best experts on this subject based on the ideXlab platform.
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coronary disease associated gene TCF21 inhibits smooth muscle cell differentiation by blocking the myocardin serum response factor pathway
Circulation Research, 2020Co-Authors: Manabu Nagao, Milos Pjanic, Trieu Nguyen, Quanyi Zhao, Paul Cheng, Robert C Wirka, Joseph M Miano, Joetsaroop S Bagga, Thomas QuertermousAbstract:Rationale: The gene encoding TCF21 (transcription factor 21) has been linked to coronary artery disease risk by human genome-wide association studies in multiple racial ethnic groups. In murine mod...
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coronary disease associated gene TCF21 inhibits smooth muscle cell differentiation by blocking the myocardin serum response factor pathway
Circulation Research, 2020Co-Authors: Manabu Nagao, Milos Pjanic, Trieu Nguyen, Quanyi Zhao, Paul Cheng, Robert C Wirka, Joetsaroop Bagga, Joseph M Miano, Thomas QuertermousAbstract:Rationale: The gene encoding transcription factor TCF21 has been linked to coronary artery disease (CAD) risk by human genome wide association studies (GWAS) in multiple racial ethnic groups. In mu...
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lncrna de novo discovery reveals noncoding rnas as major molecular mechanism associating coronary artery disease gwas variants with causal genes to confer disease risk
bioRxiv, 2019Co-Authors: Milos Pjanic, Clint L. Miller, Juyong Brian Kim, Trieu Nguyen, Quanyi Zhao, Paul Cheng, Robert C Wirka, Thomas QuertermousAbstract:Long noncoding RNAs (lncRNA) comprise an underlying regulatory network in the human genome that remains largely unexplored and could represent a molecular mechanism connecting GWAS risk variants with the disease causal genes. Human coronary artery smooth muscle cells (HCASMC) are one of the most important cells in the regulation of atherosclerotic disease progression. In this study, we aimed to discover the HCASMC-specific lncRNA collection and to explore the mechanistic relationship between HCAMSC lncRNAs with increased disease risk for coronary artery disease. We applied 6 different stimuli relevant to athero-condition, including stimulations with TGFbeta, TNFalpha, PDGFD and serum, and two transcription factor knock-downs TCF21 and SMAD3, and performed deep RNA sequencing on 48 HCASMC samples. We designed a lncRNA discovery pipeline to maximize the detection of tissue specific and low expressed lncRNAs. This generated a set of 53076 lncRNAs, that showed increased association with CAD GWAS variants, various HCASMC eQTL data sets and GTEx eQTLs for tissues enriched in smooth muscle. Module analysis revealed lncRNAs highly associated with TGFbeta and general pro-differentiation traits located in the CAD GWAS loci, such as, FES/FURIN, COL4A1/A2, CDKN2A/B, TGFB1, and FN1. Transcription factor motif analysis revealed the presence of HCASMC relevant factors, such as, TCF21, ZEB1, ZEB2, JUN, JUND, and an SRF cofactor ELK4, near the boundaries of HCASMC lncRNA. We defined lncRNA QTLs using the GTEx Coronary Artery dataset, and showed colocalization with other HCASMC QTLs, such as expression QTLs, chromatin looping QTLs, chromatin accessibility QTLs and TCF21 binding QTLs. We show several examples of CAD GWAS loci where lncRNAs show regulatory function, such as FES/FURIN, FN1, COL4A1/A2 and TGFB1. We unraveled a complex network of regulatory interactions at FES/FURIN locus, involving TCF21 and lncRNA 43779.9, and present a model in which TCF21 inhibited lncRNA 43779.9 regulates FES gene and indirectly the pro-differentiation FURIN gene by creating a looping interaction with the intron 1 of FES transcript. We define 5 regulatory variants at the FES/FURIN locus and propose a causal variant, rs35346340, that disrupts TCF21 binding and subsequently influences 43779.9 expression. Finally, we show the presence of lncRNAs in deeply sequenced TCF21 pooled ChIPSeq and discover TCF21 binding lncRNAs, 3938.1 and 3852.1 as ACTA2-regulating transcripts. This study defines lncRNAs as essential regulators of GWAS loci and shows the importance of using deep sequencing approach to further explore the genomic regulatory landscape of lncRNAs in human tissues.
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atheroprotective roles of smooth muscle cell phenotypic modulation and the TCF21 disease gene as revealed by single cell analysis
Nature Medicine, 2019Co-Authors: Milos Pjanic, Trieu Nguyen, Robert C Wirka, Dhananjay Wagh, David T Paik, Clint L. MillerAbstract:In response to various stimuli, vascular smooth muscle cells (SMCs) can de-differentiate, proliferate and migrate in a process known as phenotypic modulation. However, the phenotype of modulated SMCs in vivo during atherosclerosis and the influence of this process on coronary artery disease (CAD) risk have not been clearly established. Using single-cell RNA sequencing, we comprehensively characterized the transcriptomic phenotype of modulated SMCs in vivo in atherosclerotic lesions of both mouse and human arteries and found that these cells transform into unique fibroblast-like cells, termed 'fibromyocytes', rather than into a classical macrophage phenotype. SMC-specific knockout of TCF21-a causal CAD gene-markedly inhibited SMC phenotypic modulation in mice, leading to the presence of fewer fibromyocytes within lesions as well as within the protective fibrous cap of the lesions. Moreover, TCF21 expression was strongly associated with SMC phenotypic modulation in diseased human coronary arteries, and higher levels of TCF21 expression were associated with decreased CAD risk in human CAD-relevant tissues. These results establish a protective role for both TCF21 and SMC phenotypic modulation in this disease.
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TCF21 and ap 1 interact through epigenetic modifications to regulate coronary artery disease gene expression
Genome Medicine, 2019Co-Authors: Quanyi Zhao, Milos Pjanic, Clint L. Miller, Juyong Brian Kim, Trieu Nguyen, Manabu Nagao, Paul Cheng, Robert C Wirka, Thomas QuertermousAbstract:Genome-wide association studies have identified over 160 loci that are associated with coronary artery disease. As with other complex human diseases, risk in coronary disease loci is determined primarily by altered expression of the causal gene, due to variation in binding of transcription factors and chromatin-modifying proteins that directly regulate the transcriptional apparatus. We have previously identified a coronary disease network downstream of the disease-associated transcription factor TCF21, and in work reported here extends these studies to investigate the mechanisms by which it interacts with the AP-1 transcription complex to regulate local epigenetic effects in these downstream coronary disease loci. Genomic studies, including chromatin immunoprecipitation sequencing, RNA sequencing, and protein-protein interaction studies, were performed in human coronary artery smooth muscle cells. We show here that TCF21 and JUN regulate expression of two presumptive causal coronary disease genes, SMAD3 and CDKN2B-AS1, in part by interactions with histone deacetylases and acetyltransferases. Genome-wide TCF21 and JUN binding is jointly localized and particularly enriched in coronary disease loci where they broadly modulate H3K27Ac and chromatin state changes linked to disease-related processes in vascular cells. Heterozygosity at coronary disease causal variation, or genome editing of these variants, is associated with decreased binding of both JUN and TCF21 and loss of expression in cis, supporting a transcriptional mechanism for disease risk. These data show that the known chromatin remodeling and pioneer functions of AP-1 are a pervasive aspect of epigenetic control of transcription, and thus, the risk in coronary disease-associated loci, and that interaction of AP-1 with TCF21 to control epigenetic features, contributes to the genetic risk in loci where they co-localize.
