Quanyi Zhao

All Publications

• A cell and transcriptome atlas of human arterial vasculature. Cell genomics Zhao, Q., Pedroza, A., Sharma, D., Gu, W., Dalal, A., Weldy, C., Jackson, W., Li, D. Y., Ryan, Y., Nguyen, T., Shad, R., Palmisano, B. T., Monteiro, J. P., Worssam, M., Berezwitz, A., Iyer, M., Shi, H., Kundu, R., Limbu, L., Kim, J. B., Kundaje, A., Fischbein, M., Wirka, R., Quertermous, T., Cheng, P. 2025: 101034

  Abstract

  Arterial segments show differing disease propensities, yet mechanisms remain unknown. We compiled a transcriptomic and spatial atlas of healthy human arterial cells across multiple segments to understand these differences. Arteries demonstrated a stereotyped pattern of cell-specific, segmental heterogeneity not captured by common marker genes. Arterial identities are encoded in fibroblast and smooth muscle cell (SMC) transcriptomes. Differentially expressed genes enrich for disease loci. Fibroblast gene expression enriches for a disproportionate number of disease loci, highlighting an underrecognized role for fibroblasts in disease risk. Cells of different segments cluster more by embryonic origin than anatomy. Global analysis of disease regulons in fibroblasts and SMCs identified developmental transcription factors that persist into adulthood, suggesting a functional role of these factors in disease. Lastly, the heterogeneity of non-coding transcriptomes rivals that of protein-coding transcriptomes. Differentially expressed lncRNAs enrich for genetic signals for vascular diseases, suggesting a role for lncRNAs in vascular disease.

  View details for DOI 10.1016/j.xgen.2025.101034

  View details for PubMedID 41086809

• Smooth muscle expression of RNA editing enzyme ADAR1 controls activation of the RNA sensor MDA5 in atherosclerosis. Nature cardiovascular research Weldy, C. S., Li, Q., Monteiro, J. P., Peters, T. S., Guo, H., Galls, D., Gu, W., Cheng, P. P., Ramste, M., Li, D., Palmisano, B. T., Sharma, D., Worssam, M. D., Zhao, Q., Bhate, A., Kundu, R. K., Nguyen, T., Mokry, M., Miller, C. L., van der Laan, S. W., Li, J. B., Quertermous, T. 2025

  Abstract

  Although genetic risk in coronary artery disease (CAD) is linked to changes in gene expression, recent discoveries have revealed a major role for A-to-I RNA editing in CAD. ADAR1 edits immunogenic double-stranded RNA (dsRNA), preventing activation of the dsRNA sensor MDA5 (IFIH1) and downstream interferon-stimulated gene signaling. Using human plaque analysis and human coronary artery smooth muscle cells (SMCs), here, we show that SMCs uniquely require RNA editing and that MDA5 activation regulates SMC phenotype. In a conditional SMC-specific Adar deletion mouse model on an atherosclerosis-prone background, combined with Ifih1 deletion and single-cell RNA sequencing, we demonstrate that ADAR1 preserves vascular integrity and limits atherosclerosis and calcification by suppressing MDA5 activation. Analysis of the Athero-Express carotid endarterectomy cohort further shows that interferon-stimulated gene expression correlates with SMC modulation, plaque instability and calcification. These findings reveal a fundamental mechanism of CAD, where cell type and context-specific RNA editing modulates genetic risk and vascular disease progression.

  View details for DOI 10.1038/s44161-025-00710-5

  View details for PubMedID 40958051

  View details for PubMedCentralID 4589895

• Epigenomic landscape of single vascular cells reflects developmental origin and disease risk loci. Molecular systems biology Weldy, C. S., Kundu, S., Monteiro, J., Gu, W., Pedroza, A. J., Dalal, A. R., Worssam, M. D., Li, D., Palmisano, B., Zhao, Q., Sharma, D., Nguyen, T., Kundu, R., Fischbein, M. P., Engreitz, J., Kundaje, A. B., Cheng, P. P., Quertermous, T. 2025

  Abstract

  Vascular sites have distinct susceptibility to atherosclerosis and aneurysm, yet the epigenomic and transcriptomic underpinning of vascular site-specific disease risk is largely unknown. Here, we performed single-cell chromatin accessibility (scATACseq) and gene expression profiling (scRNAseq) of mouse vascular tissue from three vascular sites. Through interrogation of epigenomic enhancers and gene regulatory networks, we discovered key regulatory enhancers to not only be cell type, but vascular site-specific. We identified epigenetic markers of embryonic origin including developmental transcription factors such as Tbx20, Hand2, Gata4, and Hoxb family members and discovered transcription factor motif accessibility to be vascular site-specific for smooth muscle, fibroblasts, and endothelial cells. We further integrated genome-wide association data for aortic dimension, and using a deep learning model to predict variant effect on chromatin accessibility, ChromBPNet, we predicted variant effects across cell type and vascular site of origin, revealing genomic regions enriched for specific TF motif footprints-including MEF2A, SMAD3, and HAND2. This work supports a paradigm that cell type and vascular site-specific enhancers govern complex genetic drivers of disease risk.

  View details for DOI 10.1038/s44320-025-00140-2

  View details for PubMedID 40931195

  View details for PubMedCentralID 3357908

• Enhancer-targeting CRISPR screens at coronary artery disease loci suggest shared mechanisms of disease risk. medRxiv : the preprint server for health sciences Ramste, M., Weldy, C., Kundu, S., Zhao, Q., Li, D., Brand, K., Sharma, D., Ramste, A., Jagoda, E., Ray, J., Caceres, R. D., Galante, J., Gschwind, A. R., Lahtinen, N., Nguyen, T., Amrute, J. M., Park, C. Y., Kim, J. B., Kaikkonen, M. U., Stitziel, N. O., Steinmetz, L., Kundaje, A., Engreitz, J. M., Quertermous, T. 2025

  Abstract

  To systematically identify causal genetic mechanisms that confer risk for coronary artery disease (CAD) in GWAS loci, we mapped genome-wide variant-to-enhancer-to-gene (V2E2G) links in vascular smooth muscle cells (SMC). Enhancers identified by active chromatin features, and further prioritized by base-resolution deep learning models of chromatin accessibility in 108 CAD loci, were studied with CRISPRi targeting and Direct-Capture Targeted Perturb-seq (DC-TAP-seq) evaluation of 470 genes. Seventy-six V2E2G links were identified for 59 candidate CAD genes representing gene programs including epithelial-mesenchymal transformation, ubiquitination, and protein folding as well as BMP and TGFB signaling. Similar methods employed with an independent focused screen targeting one candidate locus at 9p21.3 identified 10 enhancers regulating expression of multiple genes at this location. Detailed molecular studies revealed that two enhancers mediating transcription factor binding and transcriptional regulation contribute to ancestry-specific and sex-specific risk for CAD and the surrogate biomarker vascular calcification. Together, these studies advance our identification of GWAS CAD V2E2G links across the genome, and specific mechanisms of risk at the complex 9p21.3 locus.

  View details for DOI 10.1101/2025.08.28.25334684

  View details for PubMedID 40950476

  View details for PubMedCentralID PMC12424881

• The epigenomic landscape of single vascular cells reflects developmental origin and identifies disease risk loci. bioRxiv : the preprint server for biology Weldy, C. S., Kundu, S., Monteiro, J., Gu, W., Pedroza, A. J., Dalal, A. R., Worssam, M. D., Li, D., Palmisano, B., Zhao, Q., Sharma, D., Nguyen, T., Kundu, R., Fischbein, M. P., Engreitz, J., Kundaje, A. B., Cheng, P. P., Quertermous, T. 2025

  Abstract

  Vascular sites have distinct susceptibility to atherosclerosis and aneurysm, yet the biological underpinning of vascular site-specific disease risk is largely unknown. Vascular tissues have different developmental origins that may influence global chromatin accessibility, and understanding differential chromatin accessibility, gene expression profiles, and gene regulatory networks (GRN) on single cell resolution may give key insight into vascular site-specific disease risk. Here, we performed single cell chromatin accessibility (scATACseq) and gene expression profiling (scRNAseq) of healthy adult mouse vascular tissue from three vascular sites, 1) aortic root and ascending aorta, 2) brachiocephalic and carotid artery, and 3) descending thoracic aorta. Through a comprehensive analysis at single cell resolution, we discovered key regulatory enhancers to not only be cell type, but vascular site specific in vascular smooth muscle (SMC), fibroblasts, and endothelial cells. We identified epigenetic markers of embryonic origin with differential chromatin accessibility of key developmental transcription factors such as Tbx20, Hand2, Gata4, and Hoxb family members and discovered transcription factor motif accessibility to be cell type and vascular site specific. Notably, we found ascending fibroblasts to have distinct epigenomic patterns, highlighting SMAD2/3 function to suggest a differential susceptibility to TGFβ, a finding we confirmed through in vitro culture of primary adventitial fibroblasts. Finally, to understand how vascular site-specific enhancers may regulate human genetic risk for disease, we integrated genome wide association study (GWAS) data for ascending and descending aortic dimension, and through using a distinct base resolution deep learning model to predict variant effect on chromatin accessibility, ChromBPNet, to predict variant effects in SMC, Fibroblasts, and Endothelial cells within ascending aorta, carotid, and descending aorta sites of origin. We reveal that although cell type remains a primary influence on variant effects, vascular site modifies cell type transcription and highlights genomic regions that are enriched for specific TF motif footprints - including MEF2A, SMAD3, and HAND2. This work supports a paradigm that the epigenomic and transcriptomic landscape of vascular cells are cell type and vascular site-specific and that site-specific enhancers govern complex genetic drivers of disease risk.

  View details for DOI 10.1101/2022.05.18.492517

  View details for PubMedID 40655014

  View details for PubMedCentralID PMC12247710

• Single cell variant to enhancer to gene map for coronary artery disease. medRxiv : the preprint server for health sciences Amrute, J. M., Lee, P. C., Eres, I., Lee, C. J., Bredemeyer, A., Sheth, M. U., Yamawaki, T., Gurung, R., Anene-Nzelu, C., Qiu, W. L., Kundu, S., Li, D. Y., Ramste, M., Lu, D., Tan, A., Kang, C. J., Wagoner, R. E., Alisio, A., Cheng, P., Zhao, Q., Miller, C. L., Hall, I. M., Gupta, R. M., Hsu, Y. H., Haldar, S. M., Lavine, K. J., Jackson, S., Andersson, R., Engreitz, J. M., Foo, R. S., Li, C. M., Ason, B., Quertermous, T., Stitziel, N. O. 2024

  Abstract

  Although genome wide association studies (GWAS) in large populations have identified hundreds of variants associated with common diseases such as coronary artery disease (CAD), most disease-associated variants lie within non-coding regions of the genome, rendering it difficult to determine the downstream causal gene and cell type. Here, we performed paired single nucleus gene expression and chromatin accessibility profiling from 44 human coronary arteries. To link disease variants to molecular traits, we developed a meta-map of 88 samples and discovered 11,182 single-cell chromatin accessibility quantitative trait loci (caQTLs). Heritability enrichment analysis and disease variant mapping demonstrated that smooth muscle cells (SMCs) harbor the greatest genetic risk for CAD. To capture the continuum of SMC cell states in disease, we used dynamic single cell caQTL modeling for the first time in tissue to uncover QTLs whose effects are modified by cell state and expand our insight into genetic regulation of heterogenous cell populations. Notably, we identified a variant in the COL4A1/COL4A2 CAD GWAS locus which becomes a caQTL as SMCs de-differentiate by changing a transcription factor binding site for EGR1/2. To unbiasedly prioritize functional candidate genes, we built a genome-wide single cell variant to enhancer to gene (scV2E2G) map for human CAD to link disease variants to causal genes in cell types. Using this approach, we found several hundred genes predicted to be linked to disease variants in different cell types. Next, we performed genome-wide Hi-C in 16 human coronary arteries to build tissue specific maps of chromatin conformation and link disease variants to integrated chromatin hubs and distal target genes. Using this approach, we show that rs4887091 within the ADAMTS7 CAD GWAS locus modulates function of a super chromatin interactome through a change in a CTCF binding site. Finally, we used CRISPR interference to validate a distal gene, AMOTL2, liked to a CAD GWAS locus. Collectively we provide a disease-agnostic framework to translate human genetic findings to identify pathologic cell states and genes driving disease, producing a comprehensive scV2E2G map with genetic and tissue level convergence for future mechanistic and therapeutic studies.

  View details for DOI 10.1101/2024.11.13.24317257

  View details for PubMedID 39606421

  View details for PubMedCentralID PMC11601770

• Deciphering the impact of genomic variation on function. Nature 2024; 633 (8028): 47-57

  Abstract

  Our genomes influence nearly every aspect of human biology-from molecular and cellular functions to phenotypes in health and disease. Studying the differences in DNA sequence between individuals (genomic variation) could reveal previously unknown mechanisms of human biology, uncover the basis of genetic predispositions to diseases, and guide the development of new diagnostic tools and therapeutic agents. Yet, understanding how genomic variation alters genome function to influence phenotype has proved challenging. To unlock these insights, we need a systematic and comprehensive catalogue of genome function and the molecular and cellular effects of genomic variants. Towards this goal, the Impact of Genomic Variation on Function (IGVF) Consortium will combine approaches in single-cell mapping, genomic perturbations and predictive modelling to investigate the relationships among genomic variation, genome function and phenotypes. IGVF will create maps across hundreds of cell types and states describing how coding variants alter protein activity, how noncoding variants change the regulation of gene expression, and how such effects connect through gene-regulatory and protein-interaction networks. These experimental data, computational predictions and accompanying standards and pipelines will be integrated into an open resource that will catalyse community efforts to explore how our genomes influence biology and disease across populations.

  View details for DOI 10.1038/s41586-024-07510-0

  View details for PubMedID 39232149

  View details for PubMedCentralID 7405896

• INO80-Dependent Remodeling of Transcriptional Regulatory Network Underlies the Progression of Heart Failure CIRCULATION Ren, Z., Zhao, W., Li, D., Yu, P., Mao, L., Zhao, Q., Yao, L., Zhang, X., Liu, Y., Zhou, B., Wang, L. 2024; 149 (14): 1121-1138

  Abstract

  Progressive remodeling of cardiac gene expression underlies decline in cardiac function, eventually leading to heart failure. However, the major determinants of transcriptional network switching from normal to failed hearts remain to be determined.In this study, we integrated human samples, genetic mouse models, and genomic approaches, including bulk RNA sequencing, single-cell RNA sequencing, chromatin immunoprecipitation followed by high-throughput sequencing, and assay for transposase-accessible chromatin with high-throughput sequencing, to identify the role of chromatin remodeling complex INO80 in heart homeostasis and dysfunction.The INO80 chromatin remodeling complex was abundantly expressed in mature cardiomyocytes, and its expression further increased in mouse and human heart failure. Cardiomyocyte-specific overexpression of Ino80, its core catalytic subunit, induced heart failure within 4 days. Combining RNA sequencing, chromatin immunoprecipitation followed by high-throughput sequencing, and assay for transposase-accessible chromatin with high-throughput sequencing, we revealed INO80 overexpression-dependent reshaping of the nucleosomal landscape that remodeled a core set of transcription factors, most notably the MEF2 (Myocyte Enhancer Factor 2) family, whose target genes were closely associated with cardiac function. Conditional cardiomyocyte-specific deletion of Ino80 in an established mouse model of heart failure demonstrated remarkable preservation of cardiac function.In summary, our findings shed light on the INO80-dependent remodeling of the chromatin landscape and transcriptional networks as a major mechanism underlying cardiac dysfunction in heart failure, and suggest INO80 as a potential preventative or interventional target.

  View details for DOI 10.1161/CIRCULATIONAHA.123.065440

  View details for Web of Science ID 001266179700004

  View details for PubMedID 38152931

• A single-cell atlas of Drosophila trachea reveals glycosylation-mediated Notch signaling in cell fate specification. Nature communications Li, Y., Lu, T., Dong, P., Chen, J., Zhao, Q., Wang, Y., Xiao, T., Wu, H., Zhao, Q., Huang, H. 2024; 15 (1): 2019

  Abstract

  The Drosophila tracheal system is a favorable model for investigating the program of tubular morphogenesis. This system is established in the embryo by post-mitotic cells, but also undergoes remodeling by adult stem cells. Here, we provide a comprehensive cell atlas of Drosophila trachea using the single-cell RNA-sequencing (scRNA-seq) technique. The atlas documents transcriptional profiles of tracheoblasts within the Drosophila airway, delineating 9 major subtypes. Further evidence gained from in silico as well as genetic investigations highlight a set of transcription factors characterized by their capacity to switch cell fate. Notably, the transcription factors Pebbled, Blistered, Knirps, Spalt and Cut are influenced by Notch signaling and determine tracheal cell identity. Moreover, Notch signaling orchestrates transcriptional activities essential for tracheoblast differentiation and responds to protein glycosylation that is induced by high sugar diet. Therefore, our study yields a single-cell transcriptomic atlas of tracheal development and regeneration, and suggests a glycosylation-responsive Notch signaling in cell fate determination.

  View details for DOI 10.1038/s41467-024-46455-w

  View details for PubMedID 38448482

  View details for PubMedCentralID PMC10917797

• Discovery of Transacting Long Noncoding RNAs That Regulate Smooth Muscle Cell Phenotype. Circulation research Shi, H., Nguyen, T., Zhao, Q., Cheng, P., Sharma, D., Kim, H. J., Brian Kim, J., Wirka, R., Weldy, C. S., Monteiro, J. P., Quertermous, T. 2023

  Abstract

  Smooth muscle cells (SMCs), the major cell type in atherosclerotic plaques, are vital in coronary artery diseases (CADs). Smooth muscle cell (SMC) phenotypic transition, which leads to the formation of various cell types in atherosclerotic plaques, is regulated by a network of genetic and epigenetic mechanisms and governs the risk of disease. The involvement of long noncoding RNAs (lncRNAs) has been increasingly identified in cardiovascular disease. However, SMC lncRNAs have not been comprehensively characterized, and their regulatory role in SMC state transition remains unknown.A discovery pipeline was constructed and applied to deeply strand-specific RNA sequencing from perturbed human coronary artery SMC with different disease-related stimuli, to allow for the detection of novel lncRNAs. The functional relevance of a select few novel lncRNAs were verified in vitro.We identified 4579 known and 13 655 de novo lncRNAs in human coronary artery SMC. Consistent with previous long noncoding RNA studies, these lncRNAs overall have fewer exons, are shorter in length than protein-coding genes (pcGenes), and have relatively low expression level. Genomic location of these long noncoding RNA is disproportionately enriched near CAD-related TFs (transcription factors), genetic loci, and gene regulators of SMC identity, suggesting the importance of their function in disease. Two de novo lncRNAs, ZEB-interacting suppressor (ZIPPOR) and TNS1-antisense (TNS1-AS2), were identified by our screen. Combining transcriptional data and in silico modeling along with in vitro validation, we identified CAD gene ZEB2 as a target through which these lncRNAs exert their function in SMC phenotypic transition.Expression of a large and diverse set of lncRNAs in human coronary artery SMC are highly dynamic in response to CAD-related stimuli. The dynamic changes in expression of these lncRNAs correspond to alterations in transcriptional programs that are relevant to CAD, suggesting a critical role for lncRNAs in SMC phenotypic transition and human atherosclerotic disease.

  View details for DOI 10.1161/CIRCRESAHA.122.321960

  View details for PubMedID 36852690

• Smad3 regulates smooth muscle cell fate and mediates adverse remodeling and calcification of the atherosclerotic plaque. Nature cardiovascular research Cheng, P., Wirka, R. C., Kim, J. B., Kim, H. J., Nguyen, T., Kundu, R., Zhao, Q., Sharma, D., Pedroza, A., Nagao, M., Iyer, D., Fischbein, M. P., Quertermous, T. 2022; 1 (4): 322-333

  Abstract

  Atherosclerotic plaques consist mostly of smooth muscle cells (SMC), and genes that influence SMC phenotype can modulate coronary artery disease (CAD) risk. Allelic variation at 15q22.33 has been identified by genome-wide association studies to modify the risk of CAD and is associated with the expression of SMAD3 in SMC. However, the mechanism by which this gene modifies CAD risk remains poorly understood. Here we show that SMC-specific deletion of Smad3 in a murine atherosclerosis model resulted in greater plaque burden, more outward remodelling and increased vascular calcification. Single-cell transcriptomic analyses revealed that loss of Smad3 altered SMC transition cell state toward two fates: a SMC phenotype that governs both vascular remodelling and recruitment of inflammatory cells, as well as a chondromyocyte fate. Together, the findings reveal that Smad3 expression in SMC inhibits the emergence of specific SMC phenotypic transition cells that mediate adverse plaque features, including outward remodelling, monocyte recruitment, and vascular calcification.

  View details for DOI 10.1038/s44161-022-00042-8

  View details for PubMedID 36246779

  View details for PubMedCentralID PMC9560061

• ZEB2 Shapes the Epigenetic Landscape of Atherosclerosis Circulation Cheng, P., Wirka, R. C., Clarke, L., Zhao, Q., Kundu, R., Nguyen, T., Nair, S., Sharma, D., Kim, H., Shi, H., Assimes, T., Kim, J., Kundaje, A., Quertermous, T. 2022; 145 (6): 469–485

  Abstract

  Background: Smooth muscle cells (SMC) transition into a number of different phenotypes during atherosclerosis, including those that resemble fibroblasts and chondrocytes, and make up the majority of cells in the atherosclerotic plaque. To better understand the epigenetic and transcriptional mechanisms that mediate these cell state changes, and how they relate to risk for coronary artery disease (CAD), we have investigated the causality and function of transcription factors (TFs) at genome wide associated loci. Methods: We employed CRISPR-Cas 9 genome and epigenome editing to identify the causal gene and cell(s) for a complex CAD GWAS signal at 2q22.3. Subsequently, single-cell epigenetic and transcriptomic profiling in murine models and human coronary artery smooth muscle cells were employed to understand the cellular and molecular mechanism by which this CAD risk gene exerts its function. Results: CRISPR-Cas 9 genome and epigenome editing showed that the complex CAD genetic signals within a genomic region at 2q22.3 lie within smooth muscle long-distance enhancers for ZEB2, a TF extensively studied in the context of epithelial mesenchymal transition (EMT) in development and cancer. ZEB2 regulates SMC phenotypic transition through chromatin remodeling that obviates accessibility and disrupts both Notch and TGFβ signaling, thus altering the epigenetic trajectory of SMC transitions. SMC specific loss of ZEB2 resulted in an inability of transitioning SMCs to turn off contractile programing and take on a fibroblast-like phenotype, but accelerated the formation of chondromyocytes, mirroring features of high-risk atherosclerotic plaques in human coronary arteries. Conclusions: These studies identify ZEB2 as a new CAD GWAS gene that affects features of plaque vulnerability through direct effects on the epigenome, providing a new thereapeutic approach to target vascular disease.

  View details for DOI 10.1161/CIRCULATIONAHA.121.057789

• Molecular mechanisms of coronary disease revealed using quantitative trait loci for TCF21 binding, chromatin accessibility, and chromosomal looping. Genome biology Zhao, Q. n., Dacre, M. n., Nguyen, T. n., Pjanic, M. n., Liu, B. n., Iyer, D. n., Cheng, P. n., Wirka, R. n., Kim, J. B., Fraser, H. B., Quertermous, T. n. 2020; 21 (1): 135

  Abstract

  To investigate the epigenetic and transcriptional mechanisms of coronary artery disease (CAD) risk, as well as the functional regulation of chromatin structure and function, we create a catalog of genetic variants associated with three stages of transcriptional cis-regulation in primary human coronary artery vascular smooth muscle cells (HCASMCs).We use a pooling approach with HCASMC lines to map regulatory variants that mediate binding of the CAD-associated transcription factor TCF21 with ChIPseq studies (bQTLs), variants that regulate chromatin accessibility with ATACseq studies (caQTLs), and chromosomal looping with Hi-C methods (clQTLs). We examine the overlap of these QTLs and their relationship to smooth muscle-specific genes and transcription factors. Further, we use multiple analyses to show that these QTLs are highly associated with CAD GWAS loci and correlate to lead SNPs where they show allelic effects. By utilizing genome editing, we verify that identified functional variants can regulate both chromatin accessibility and chromosomal looping, providing new insights into functional mechanisms regulating chromatin state and chromosomal structure. Finally, we directly link the disease-associated TGFB1-SMAD3 pathway to the CAD-associated FN1 gene through a response QTL that modulates both chromatin accessibility and chromosomal looping.Together, these studies represent the most thorough mapping of multiple QTL types in a highly disease-relevant primary cultured cell type and provide novel insights into their functional overlap and mechanisms that underlie these genomic features and their relationship to disease risk.

  View details for DOI 10.1186/s13059-020-02049-5

  View details for PubMedID 32513244

• The Environment-Sensing Aryl-Hydrocarbon Receptor Inhibits the Chondrogenic Fate of Modulated Smooth Muscle Cells in Atherosclerotic Lesions. Circulation Kim, J. B., Zhao, Q. n., Nguyen, T. n., Pjanic, M. n., Cheng, P. n., Wirka, R. n., Travisano, S. n., Nagao, M. n., Kundu, R. n., Quertermous, T. n. 2020

  Abstract

  Background: Smooth muscle cells (SMC) play a critical role in atherosclerosis. The Aryl hydrocarbon receptor (AHR) is an environment-sensing transcription factor that contributes to vascular development, and has been implicated in coronary artery disease (CAD) risk. We hypothesized that AHR can affect atherosclerosis by regulating phenotypic modulation of SMC. Methods: We combined RNA-Seq, ChIP-Seq, ATAC-Seq and in-vitro assays in human coronary artery SMC (HCASMC), with single-cell RNA-Seq (scRNA-Seq), histology, and RNAscope in an SMC-specific lineage-tracing Ahr knockout mouse model of atherosclerosis to better understand the role of AHR in vascular disease. Results: Genomic studies coupled with functional assays in cultured HCASMC revealed that AHR modulates HCASMC phenotype and suppresses ossification in these cells. Lineage tracing and activity tracing studies in the mouse aortic sinus showed that the Ahr pathway is active in modulated SMC in the atherosclerotic lesion cap. Furthermore, scRNA-Seq studies of the SMC-specific Ahr knockout mice showed a significant increase in the proportion of modulated SMC expressing chondrocyte markers such as Col2a1 and Alpl, which localized to the lesion neointima. These cells, which we term "chondromyocytes" (CMC), were also identified in the neointima of human coronary arteries. In histological analyses, these changes manifested as larger lesion size, increased lineage-traced SMC participation in the lesion, decreased lineage-traced SMC in the lesion cap, and increased alkaline phosphatase activity in lesions in the Ahr knockout compared to wild-type mice. We propose that AHR is likely protective based on these data and inference from human genetic analyses. Conclusions: Overall, we conclude that AHR promotes maintenance of lesion cap integrity and diminishes the disease related SMC-to-CMC transition in atherosclerotic tissues.

  View details for DOI 10.1161/CIRCULATIONAHA.120.045981

  View details for PubMedID 32441123

• Coronary Disease Associated Gene TCF21 Inhibits Smooth Muscle Cell Differentiation by Blocking the Myocardin-Serum Response Factor Pathway. Circulation research Nagao, M., Lyu, Q., Zhao, Q., Wirka, R. C., Bagga, J., Nguyen, T., Cheng, P., Kim, J. B., Pjanic, M., Miano, J. M., Quertermous, T. 2019

  Abstract

  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 murine models, Tcf21 is required for phenotypic modulation of smooth muscle cells (SMC) in atherosclerotic tissues and promotes a fibroblast phenotype in these cells. In humans, TCF21 expression inhibits risk for CAD. The molecular mechanism by which TCF21 regulates SMC phenotype is not known. Objective: To better understand how TCF21 affects SMC phenotype, we sought to investigate the possible mechanisms by which it regulates the lineage determining myocardin (MYOCD)-serum response factor (SRF) pathway. Methods and Results: Modulation of TCF21 expression in HCASMC revealed that TCF21 suppresses a broad range of SMC markers, as well as key SMC transcription factors MYOCD and SRF, at the RNA and protein level. We conducted chromatin immunoprecipitation (ChIP)-sequencing to map SRF binding sites in HCASMC, showing that binding is colocalized in the genome with TCF21, including at a novel enhancer in the SRF gene, and at the MYOCD gene promoter. In vitro genome editing indicated that the SRF enhancer CArG box regulates transcription of the SRF gene, and mutation of this conserved motif in the orthologous mouse SRF enhancer revealed decreased SRF expression in aorta and heart tissues. Direct TCF21 binding and transcriptional inhibition at co-localized sites were established by reporter gene transfection assays. Chromatin immunoprecipitation and protein co-immunoprecipitation studies provided evidence that TCF21 blocks MYOCD and SRF association by direct TCF21-MYOCD interaction. Conclusions: These data indicate that TCF21 antagonizes the MYOCD-SRF pathway through multiple mechanisms, further establishing a role for this CAD associated gene in fundamental SMC processes and indicating the importance of smooth muscle response to vascular stress and phenotypic modulation of this cell type in CAD risk.

  View details for DOI 10.1161/CIRCRESAHA.119.315968

  View details for PubMedID 31815603

• TCF21 and AP-1 interact through epigenetic modifications to regulate coronary artery disease gene expression. Genome medicine Zhao, Q. n., Wirka, R. n., Nguyen, T. n., Nagao, M. n., Cheng, P. n., Miller, C. L., Kim, J. B., Pjanic, M. n., Quertermous, T. n. 2019; 11 (1): 23

  Abstract

  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.

  View details for PubMedID 31014396

• Coronary artery disease genes SMAD3 and TCF21 promote opposing interactive genetic programs that regulate smooth muscle cell differentiation and disease risk PLOS GENETICS Iyer, D., Zhao, Q., Wirka, R., Naravane, A., Trieu Nguyen, Liu, B., Nagao, M., Cheng, P., Miller, C. L., Kim, J., Pjanic, M., Quertermous, T. 2018; 14 (10)

  View details for DOI 10.1371/journal.pgen.1007681

  View details for Web of Science ID 000449328500019

• The EZH1-SUZ12 complex positively regulates the transcription of NF-κB target genes through interaction with UXT JOURNAL OF CELL SCIENCE Su, S., Li, C., Lei, P., Wang, X., Zhao, Q., Cai, Y., Wang, Z., Li, L., Wu, M. 2016; 129 (12): 2343-2353

  Abstract

  Unlike other members of the polycomb group protein family, EZH1 has been shown to positively associate with active transcription on a genome-wide scale. However, the underlying mechanism for this behavior still remains elusive. Here, we report that EZH1 physically interacts with UXT, a small chaperon-like transcription co-activator. UXT specifically interacts with EZH1 and SUZ12, but not EED. Similar to upon knockdown of UXT, knockdown of EZH1 or SUZ12 through RNA interference in the cell impairs the transcriptional activation of nuclear factor (NF)-κB target genes induced by TNFα. EZH1 deficiency also increases TNFα-induced cell death. Interestingly, chromatin immunoprecipitation and the following next-generation sequencing analysis show that H3K27 mono-, di- and tri-methylation on NF-κB target genes are not affected in EZH1- or UXT-deficient cells. EZH1 also does not affect the translocation of the p65 subunit of NF-κB (also known as RELA) from the cytosol to the nucleus. Instead, EZH1 and SUZ12 regulate the recruitment of p65 and RNA Pol II to target genes. Taken together, our study shows that EZH1 and SUZ12 act as positive regulators for NF-κB signaling and demonstrates that EZH1, SUZ12 and UXT work synergistically to regulate pathway activation in the nucleus.

  View details for DOI 10.1242/jcs.185546

  View details for Web of Science ID 000379498500007

  View details for PubMedID 27127229

• Global histone modification profiling reveals the epigenomic dynamics during malignant transformation in a four-stage breast cancer model CLINICAL EPIGENETICS Zhao, Q., Lei, P., Zhang, X., Zheng, J., Wang, H., Zhao, J., Li, Y., Ye, M., Li, L., Wei, G., Wu, M. 2016; 8: 34

  Abstract

  Epigenetic regulation has emerged to be the critical steps for tumorigenesis and metastasis. Multiple histone methyltransferase and demethylase have been implicated as tumor suppressors or oncogenes recently. But the key epigenomic events in cancer cell transformation still remain poorly understood.A breast cancer transformation model was established via stably expressing three oncogenes in primary breast epithelial cells. Chromatin immunoprecipitation followed by the next-generation sequencing of histone methylations was performed to determine epigenetic events during transformation. Western blot, quantitative RT-PCR, and immunostaining were used to determine gene expression in cells and tissues.Histones H3K9me2 and me3, two repressive marks of transcription, decrease in in vitro breast cancer cell model and in vivo clinical tissues. A survey of enzymes related with H3K9 methylation indicated that KDM3A/JMJD1A, a demethylase for H3K9me1 and me2, gradually increases during cancer transformation and is elevated in patient tissues. KDM3A/JMJD1A deficiency impairs the growth of tumors in nude mice and transformed cell lines. Genome-wide ChIP-seq analysis reveals that the boundaries of decreased H3K9me2 large organized chromatin K9 modifications (LOCKs) are enriched with cancer-related genes, such as MYC and PAX3. Further studies show that KDM3A/JMJD1A directly binds to these oncogenes and regulates their transcription by removing H3K9me2 mark.Our study demonstrates reduction of histones H3K9 me2 and me3, and elevation of KDM3A/JMJD1A as important events for breast cancer, and illustrates the dynamic epigenomic mechanisms during breast cancer transformation.

  View details for DOI 10.1186/s13148-016-0201-x

  View details for Web of Science ID 000373261600001

  View details for PubMedID 27034728

  View details for PubMedCentralID PMC4815258