BACH1 deficiency prevents neointima formation and maintains the differentiated phenotype of vascular smooth muscle cells by regulating chromatin accessibility

Abstract The transcription factor BTB and CNC homology 1(BACH1) has been linked to coronary artery disease risk by human genome-wide association studies, but little is known about the role of BACH1 in vascular smooth muscle cell (VSMC) phenotype switching and neointima formation following vascular injury. Therefore, this study aims to explore the role of BACH1 in vascular remodeling and its underlying mechanisms. BACH1 was highly expressed in human atherosclerotic plaques and has high transcriptional factor activity in VSMCs of human atherosclerotic arteries. VSMC-specific loss of Bach1 in mice inhibited the transformation of VSMC from contractile to synthetic phenotype and VSMC proliferation and attenuated the neointimal hyperplasia induced by wire injury. Mechanistically, BACH1 suppressed chromatin accessibility at the promoters of VSMC marker genes via recruiting histone methyltransferase G9a and cofactor YAP and maintaining the H3K9me2 state, thereby repressing VSMC marker genes expression in human aortic smooth muscle cells (HASMCs). BACH1-induced repression of VSMC marker genes was abolished by the silencing of G9a or YAP. Thus, these findings demonstrate a crucial regulatory role of BACH1 in VSMC phenotypic transition and vascular homeostasis and shed light on potential future protective vascular disease intervention via manipulation of BACH1.

[1]  Brad T. Sherman,et al.  DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update) , 2022, Nucleic Acids Res..

[2]  Jianyi(Jay) Zhang,et al.  Deletion of BACH1 Attenuates Atherosclerosis by Reducing Endothelial Inflammation , 2022, Circulation research.

[3]  T. Lönnberg,et al.  Single-Cell Epigenomics and Functional Fine-Mapping of Atherosclerosis GWAS Loci , 2021, Circulation research.

[4]  J. Han,et al.  BACH1 recruits NANOG and histone H3 lysine 4 methyltransferase MLL/SET1 complexes to regulate enhancer–promoter activity and maintains pluripotency , 2021, Nucleic acids research.

[5]  Zhen-Ge Luo,et al.  TBC1D3 promotes neural progenitor proliferation by suppressing the histone methyltransferase G9a , 2021, Science Advances.

[6]  K. Zhao,et al.  The epigenetic basis of cellular heterogeneity , 2020, Nature Reviews Genetics.

[7]  Jorja G Henikoff,et al.  Efficient low-cost chromatin profiling with CUT&Tag , 2020, Nature Protocols.

[8]  T. Quertermous,et al.  Environment-Sensing Aryl Hydrocarbon Receptor Inhibits the Chondrogenic Fate of Modulated Smooth Muscle Cells in Atherosclerotic Lesions , 2020, Circulation.

[9]  K. Song,et al.  The Histone Methyltransferase G9a Promotes Cholangiocarcinogenesis through Regulation of the Hippo Pathway Kinase LATS2 and YAP Signaling Pathway , 2020, The FASEB Journal.

[10]  Christian H. Holland,et al.  Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data , 2020, Genome Biology.

[11]  Wei Yue,et al.  Semi-quantitative Determination of Protein Expression using Immunohistochemistry Staining and Analysis: An Integrated Protocol. , 2019, Bio-protocol.

[12]  T. Quertermous,et al.  Coronary Disease-Associated Gene TCF21 Inhibits Smooth Muscle Cell Differentiation by Blocking the Myocardin-Serum Response Factor Pathway , 2019, Circulation research.

[13]  Phillip A. Richmond,et al.  JASPAR 2020: update of the open-access database of transcription factor binding profiles , 2019, Nucleic Acids Res..

[14]  Ralitsa R. Madsen,et al.  Epigenetic Regulation of Vascular Smooth Muscle Cells by Histone H3 Lysine 9 Dimethylation Attenuates Target Gene-Induction by Inflammatory Signaling , 2019, Arteriosclerosis, thrombosis, and vascular biology.

[15]  Clint L. Miller,et al.  Atheroprotective roles of smooth muscle cell phenotypic modulation and the TCF21 disease gene as revealed by single-cell analysis , 2019, Nature Medicine.

[16]  T. Corson,et al.  Small-Molecule Covalent Modification of Conserved Cysteine Leads to Allosteric Inhibition of the TEAD⋅Yap Protein-Protein Interaction. , 2019, Cell chemical biology.

[17]  Matthew C. Hill,et al.  YAP Partially Reprograms Chromatin Accessibility to Directly Induce Adult Cardiogenesis In Vivo. , 2019, Developmental cell.

[18]  Sandy L. Klemm,et al.  Chromatin accessibility and the regulatory epigenome , 2019, Nature Reviews Genetics.

[19]  Christoph Hafemeister,et al.  Comprehensive integration of single cell data , 2018, bioRxiv.

[20]  Cong Niu,et al.  Bach1: Function, Regulation, and Involvement in Disease , 2018, Oxidative medicine and cellular longevity.

[21]  L. Litovchick Resolving Proteins for Immunoblotting by Gel Electrophoresis. , 2018, Cold Spring Harbor Protocols.

[22]  Andrew C. Adey,et al.  Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data. , 2018, Molecular cell.

[23]  Zev J. Gartner,et al.  DoubletFinder: Doublet detection in single-cell RNA sequencing data using artificial nearest neighbors , 2018, bioRxiv.

[24]  Shuang He,et al.  Yes-Associated Protein Promotes Angiogenesis via Signal Transducer and Activator of Transcription 3 in Endothelial Cells , 2018, Circulation research.

[25]  Pim van der Harst,et al.  Identification of 64 Novel Genetic Loci Provides an Expanded View on the Genetic Architecture of Coronary Artery Disease , 2017, Circulation research.

[26]  K. Guan,et al.  Regulation of the Hippo Pathway Transcription Factor TEAD. , 2017, Trends in biochemical sciences.

[27]  Nicholas A. Sinnott-Armstrong,et al.  An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues , 2017, Nature Methods.

[28]  William J. Greenleaf,et al.  chromVAR: Inferring transcription factor-associated accessibility from single-cell epigenomic data , 2017, Nature Methods.

[29]  Jianyi(Jay) Zhang,et al.  The Transcription Factor Bach1 Suppresses the Developmental Angiogenesis of Zebrafish , 2017, Oxidative medicine and cellular longevity.

[30]  Jiao Jiao,et al.  Yes‐Associated Protein Inhibits Transcription of Myocardin and Attenuates Differentiation of Vascular Smooth Muscle Cell from Cardiovascular Progenitor Cell Lineage , 2017, Stem cells.

[31]  N. Gray,et al.  Pharmacological targeting of kinases MST1 and MST2 augments tissue repair and regeneration , 2016, Science Translational Medicine.

[32]  Alicia N. Schep,et al.  Nfib Promotes Metastasis through a Widespread Increase in Chromatin Accessibility , 2016, Cell.

[33]  R. Mostoslavsky,et al.  Interplay between Metabolism and Epigenetics: A Nuclear Adaptation to Environmental Changes. , 2016, Molecular cell.

[34]  Xin Hu,et al.  Suppression of Enhancer Overactivation by a RACK7-Histone Demethylase Complex , 2016, Cell.

[35]  M. Bennett,et al.  Vascular Smooth Muscle Cells in Atherosclerosis. , 2016, Circulation research.

[36]  Minoru Kanehisa,et al.  KEGG as a reference resource for gene and protein annotation , 2015, Nucleic Acids Res..

[37]  A. Zernecke,et al.  Alternation of histone and DNA methylation in human atherosclerotic carotid plaques , 2015, Thrombosis and Haemostasis.

[38]  B. Garcia,et al.  A specific LSD1/KDM1A isoform regulates neuronal differentiation through H3K9 demethylation. , 2015, Molecular cell.

[39]  Steven L Salzberg,et al.  HISAT: a fast spliced aligner with low memory requirements , 2015, Nature Methods.

[40]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[41]  Yong Ho Bae,et al.  A FAK-Cas-Rac-Lamellipodin Signaling Module Transduces Extracellular Matrix Stiffness into Mechanosensitive Cell Cycling , 2014, Science Signaling.

[42]  N. Penrod,et al.  Methyltransferase G9A regulates T cell differentiation during murine intestinal inflammation. , 2014, The Journal of clinical investigation.

[43]  Cole Trapnell,et al.  The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells , 2014, Nature Biotechnology.

[44]  Fang Liu,et al.  Deletion of Yes-Associated Protein (YAP) Specifically in Cardiac and Vascular Smooth Muscle Cells Reveals a Crucial Role for YAP in Mouse Cardiovascular Development , 2014, Circulation research.

[45]  Guoqing Hu,et al.  The Induction of Yes-Associated Protein Expression After Arterial Injury Is Crucial for Smooth Muscle Phenotypic Modulation and Neointima Formation , 2012, Arteriosclerosis, thrombosis, and vascular biology.

[46]  Yong Zhang,et al.  Identifying ChIP-seq enrichment using MACS , 2012, Nature Protocols.

[47]  Qiwei Yang,et al.  BIX‐01294 treatment blocks cell proliferation, migration and contractility in ovine foetal pulmonary arterial smooth muscle cells , 2012, Cell proliferation.

[48]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[49]  David R. Kelley,et al.  Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks , 2012, Nature Protocols.

[50]  T. Borodina,et al.  The BTB and CNC Homology 1 (BACH1) Target Genes Are Involved in the Oxidative Stress Response and in Control of the Cell Cycle* , 2011, The Journal of Biological Chemistry.

[51]  Y. Shinkai,et al.  H3K9 methyltransferase G9a and the related molecule GLP. , 2011, Genes & development.

[52]  Zhou Yu,et al.  Microsomal Prostaglandin E2 Synthase-1 Modulates the Response to Vascular Injury , 2011, Circulation.

[53]  C. Glass,et al.  Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. , 2010, Molecular cell.

[54]  Rachael P. Huntley,et al.  QuickGO: a web-based tool for Gene Ontology searching , 2009, Bioinform..

[55]  M. Toyofuku,et al.  Effects of genetic ablation of bach1 upon smooth muscle cell proliferation and atherosclerosis after cuff injury , 2005, Genes to cells : devoted to molecular & cellular mechanisms.

[56]  O. McDonald,et al.  A G/C Element Mediates Repression of the SM22&agr; Promoter Within Phenotypically Modulated Smooth Muscle Cells in Experimental Atherosclerosis , 2004, Circulation research.

[57]  G. Owens,et al.  Molecular regulation of vascular smooth muscle cell differentiation in development and disease. , 2004, Physiological reviews.

[58]  H. Kato,et al.  G9a histone methyltransferase plays a dominant role in euchromatic histone H3 lysine 9 methylation and is essential for early embryogenesis. , 2002, Genes & development.

[59]  E. Ito,et al.  The promoter of mouse transcription repressor bach1 is regulated by Sp1 and trans-activated by Bach1. , 2001, Journal of Biochemistry (Tokyo).