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Song XW, He WX, Su T, Li CJ, Jiang LL, Huang SQ, Li SH, Guo ZF, Zhang BL. Abnormal expression of PRKAG2-AS1 in endothelial cells induced inflammation and apoptosis by reducing PRKAG2 expression. Noncoding RNA Res 2024; 9:536-546. [PMID: 38511052 PMCID: PMC10950609 DOI: 10.1016/j.ncrna.2024.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 02/07/2024] [Accepted: 02/20/2024] [Indexed: 03/22/2024] Open
Abstract
PRKAG2 is required for the maintenance of cellular energy balance. PRKAG2-AS1, a long non-coding RNA (lncRNA), was found within the promoter region of PRKAG2. Despite the extensive expression of PRKAG2-AS1 in endothelial cells, the precise function and mechanism of this gene in endothelial cells have yet to be elucidated. The localization of PRKAG2-AS1 was predominantly observed in the nucleus, as revealed using nuclear and cytoplasmic fractionation and fluorescence in situ hybridization. The manipulation of PRKAG2-AS1 by knockdown and overexpression within the nucleus significantly altered PRKAG2 expression in a cis-regulatory manner. The expression of PRKAG2-AS1 and its target genes, PRKAG2b and PRKAG2d, was down-regulated in endothelial cells subjected to oxLDL and Hcy-induced injury. This finding suggests that PRKAG2-AS1 may be involved in the mechanism behind endothelial injury. The suppression of PRKAG2-AS1 specifically in the nucleus led to an upregulation of inflammatory molecules such as cytokines, adhesion molecules, and chemokines in endothelial cells. Additionally, this nuclear suppression of PRKAG2-AS1 facilitated the adherence of THP1 cells to endothelial cells. We confirmed the role of nuclear knockdown PRKAG2-AS1 in the induction of apoptosis and inhibition of cell proliferation, migration, and lumen formation through flow cytometry, TUNEL test, CCK8 assay, and cell scratching. Finally, it was determined that PRKAG2-AS1 exerts direct control over the transcription of PRKAG2 by its binding to their promoters. In conclusion, downregulation of PRKAG2-AS1 suppressed the proliferation and migration, promoted inflammation and apoptosis of endothelial cells, and thus contributed to the development of atherosclerosis resulting from endothelial cell injury.
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Affiliation(s)
- Xiao-Wei Song
- Department of Anesthesiology, Shidong Hospital of Shanghai, University of Shanghai for Science and Technology, Shanghai, China
- Department of Cardiology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Wen-Xia He
- Department of Cardiology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Ting Su
- Department of Cardiology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Chang-Jin Li
- Department of Cardiology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Li-Li Jiang
- Department of Cardiology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Song-Qun Huang
- Department of Cardiology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Song-Hua Li
- Department of Cardiology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Zhi-Fu Guo
- Department of Cardiology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Bi-Li Zhang
- Department of Cardiology, Changhai Hospital, Second Military Medical University, Shanghai, China
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Luo J, Chen Z, Qiao Y, Tien JCY, Young E, Mannan R, Mahapatra S, He T, Eyunni S, Zhang Y, Zheng Y, Su F, Cao X, Wang R, Cheng Y, Seri R, George J, Shahine M, Miner SJ, Vaishampayan U, Wang M, Wang S, Parolia A, Chinnaiyan AM. p300/CBP degradation is required to disable the active AR enhanceosome in prostate cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.29.587346. [PMID: 38586029 PMCID: PMC10996709 DOI: 10.1101/2024.03.29.587346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Prostate cancer is an exemplar of an enhancer-binding transcription factor-driven disease. The androgen receptor (AR) enhanceosome complex comprised of chromatin and epigenetic coregulators assembles at enhancer elements to drive disease progression. The paralog lysine acetyltransferases p300 and CBP deposit histone marks that are associated with enhancer activation. Here, we demonstrate that p300/CBP are determinant cofactors of the active AR enhanceosome in prostate cancer. Histone H2B N-terminus multisite lysine acetylation (H2BNTac), which is exclusively reliant on p300/CBP catalytic function, marked active enhancers and was notably elevated in prostate cancer lesions relative to the adjacent benign epithelia. Degradation of p300/CBP rapidly depleted acetylation marks associated with the active AR enhanceosome, which was only partially phenocopied by inhibition of their reader bromodomains. Notably, H2BNTac was effectively abrogated only upon p300/CBP degradation, which led to a stronger suppression of p300/CBP-dependent oncogenic gene programs relative to bromodomain inhibition or the inhibition of its catalytic domain. In vivo experiments using an orally active p300/CBP proteolysis targeting chimera (PROTAC) degrader (CBPD-409) showed that p300/CBP degradation potently inhibited tumor growth in preclinical models of castration-resistant prostate cancer and synergized with AR antagonists. While mouse p300/CBP orthologs were effectively degraded in host tissues, prolonged treatment with the PROTAC degrader was well tolerated with no significant signs of toxicity. Taken together, our study highlights the pivotal role of p300/CBP in maintaining the active AR enhanceosome and demonstrates how target degradation may have functionally distinct effects relative to target inhibition, thus supporting the development of p300/CBP degraders for the treatment of advanced prostate cancer.
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Vellingiri V, Balaji Ragunathrao VA, Joshi JC, Akhter MZ, Anwar M, Banerjee S, Dudek S, Tsukasaki Y, Pinho S, Mehta D. Endothelial ERG programs neutrophil transcriptome for sustained anti-inflammatory vascular niche. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.02.591799. [PMID: 38746216 PMCID: PMC11092576 DOI: 10.1101/2024.05.02.591799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Neutrophils (PMNs) reside as a marginated pool within the vasculature, ready for deployment during infection. However, how endothelial cells (ECs) control PMN extravasation and activation to strengthen tissue homeostasis remains ill-defined. Here, we found that the vascular ETS-related gene (ERG) is a generalized mechanism regulating PMN activity in preclinical tissue injury models and human patients. We show that ERG loss in ECs rewired PMN-transcriptome, enriched for genes associated with the CXCR2-CXCR4 signaling. Rewired PMNs compromise mice survival after pneumonia and induced lung vascular inflammatory injury following adoptive transfer into naïve mice, indicating their longevity and inflammatory activity memory. Mechanistically, EC-ERG restricted PMN extravasation and activation by upregulating the deubiquitinase A20 and downregulating the NFκB-IL8 cascade. Rescuing A20 in EC-Erg -/- endothelium or suppressing PMN-CXCR2 signaling rescued EC control of PMN activation. Findings deepen our understanding of EC control of PMN-mediated inflammation, offering potential avenues for targeting various inflammatory diseases. Highlights ERG regulates trans-endothelial neutrophil (PMN) extravasation, retention, and activationLoss of endothelial (EC) ERG rewires PMN-transcriptomeAdopted transfer of rewired PMNs causes inflammation in a naïve mouse ERG transcribes A20 and suppresses CXCR2 function to inactivate PMNs. In brief/blurb The authors investigated how vascular endothelial cells (EC) control polymorphonuclear neutrophil (PMN) extravasation, retention, and activation to strengthen tissue homeostasis. They showed that EC-ERG controls PMN transcriptome into an anti-adhesive and anti-inflammatory lineage by synthesizing A20 and suppressing PMNs-CXCR2 signaling, defining EC-ERG as a target for preventing neutrophilic inflammatory injury.
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Aurigemma I, Lanzetta O, Cirino A, Allegretti S, Lania G, Ferrentino R, Poondi Krishnan V, Angelini C, Illingworth E, Baldini A. Endothelial gene regulatory elements associated with cardiopharyngeal lineage differentiation. Commun Biol 2024; 7:351. [PMID: 38514806 PMCID: PMC10957928 DOI: 10.1038/s42003-024-06017-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 03/06/2024] [Indexed: 03/23/2024] Open
Abstract
Endothelial cells (EC) differentiate from multiple sources, including the cardiopharyngeal mesoderm, which gives rise also to cardiac and branchiomeric muscles. The enhancers activated during endothelial differentiation within the cardiopharyngeal mesoderm are not completely known. Here, we use a cardiogenic mesoderm differentiation model that activates an endothelial transcription program to identify endothelial regulatory elements activated in early cardiogenic mesoderm. Integrating chromatin remodeling and gene expression data with available single-cell RNA-seq data from mouse embryos, we identify 101 putative regulatory elements of EC genes. We then apply a machine-learning strategy, trained on validated enhancers, to predict enhancers. Using this computational assay, we determine that 50% of these sequences are likely enhancers, some of which are already reported. We also identify a smaller set of regulatory elements of well-known EC genes and validate them using genetic and epigenetic perturbation. Finally, we integrate multiple data sources and computational tools to search for transcriptional factor binding motifs. In conclusion, we show EC regulatory sequences with a high likelihood to be enhancers, and we validate a subset of them using computational and cell culture models. Motif analyses show that the core EC transcription factors GATA/ETS/FOS is a likely driver of EC regulation in cardiopharyngeal mesoderm.
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Affiliation(s)
- Ilaria Aurigemma
- PhD program in Molecular Medicine and Medical Biotechnology, University Federico II, Via Sergio Pansini 5, 80131, Naples, Italy
- Department of Chemistry and Biology, University of Salerno, Via Giovanni Paolo II 132, 84084, Fisciano, Italy
| | - Olga Lanzetta
- Institute of Genetics and Biophysics, National Research Council, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Andrea Cirino
- Institute of Genetics and Biophysics, National Research Council, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Sara Allegretti
- PhD program in Molecular Medicine and Medical Biotechnology, University Federico II, Via Sergio Pansini 5, 80131, Naples, Italy
| | - Gabriella Lania
- Institute of Genetics and Biophysics, National Research Council, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Rosa Ferrentino
- Institute of Genetics and Biophysics, National Research Council, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Varsha Poondi Krishnan
- Institute of Genetics and Biophysics, National Research Council, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Claudia Angelini
- Istituto Applicazioni del Calcolo, National Research Council, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Elizabeth Illingworth
- Department of Chemistry and Biology, University of Salerno, Via Giovanni Paolo II 132, 84084, Fisciano, Italy
| | - Antonio Baldini
- PhD program in Molecular Medicine and Medical Biotechnology, University Federico II, Via Sergio Pansini 5, 80131, Naples, Italy.
- Department of Molecular Medicine and Medical Biotechnology, University Federico II, Via Sergio Pansini 5, 80131, Naples, Italy.
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Liu J, Chen C, Qin X, Wang J, Zhang B, Jin F. Plasma-derived exosomes contributes to endothelial-to-mesenchymal transition in Moyamoya disease. Heliyon 2024; 10:e26748. [PMID: 38434376 PMCID: PMC10907668 DOI: 10.1016/j.heliyon.2024.e26748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 01/31/2024] [Accepted: 02/19/2024] [Indexed: 03/05/2024] Open
Abstract
Background Moyamoya disease (MMD) is a cerebrovascular disease with a high disability rate; however, its pathogenesis remains unknown. Endothelial-mesenchymal transition (EndMT) is the pathological basis of many vascular diseases; however, the key role of EndMT in MMD has not yet been reported. Method We collected vascular tissues from three control samples and six patients with MMD to detect the expression of EndMT-related genes. To elucidate the mechanism of EndMT in MMD, we performed in vitro cell experiments. Plasma-derived exosomes (PDEs) can transmit information between cells and tissues and are of considerable importance in several disease studies. PDEs were used to stimulate EndMT phenotype in cerebrovascular endothelial cells. Results Multiplex fluorescent immunohistochemistry staining confirmed that CD31, VE-cadherin and E-cadherin down-regulated, whereas α-SMA and vimentin were significantly up-regulated in moyamoya vascular endothelial cells than in control samples. PDEs from MMD patients significantly promoted cell proliferation and migration, resulting in slender cells. PDEs induce EndMT-related phenotype changes in cerebral vascular endothelial cells, including decreased endothelial cell marker expression and increased mesenchymal cell marker expression. We demonstrated that EndMT phenotypic alterations are mediated, in part, by microRNA(miRNAs). Conclusion This study was the first to propose that EndMT may exist in the vessels of patients with MMD. PDEs induce the EndMT phenotype to promote the development of MMD. This study aimed to provide a new theoretical basis for elucidating the pathogenesis of MMD.
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Affiliation(s)
- Jilan Liu
- Department of Medical Research Center, Affiliated Hospital of Jining Medical University, Jining, Shandong, 272029, PR China
| | - Chao Chen
- Department of Neurosurgery, Qingdao Central Hospital, University of Health and Rehabilitation Sciences &Qingdao Central Hospital Medical Group, Qingdao, Shandong, 266042, PR China
| | - Xianyun Qin
- Department of Medical Research Center, Affiliated Hospital of Jining Medical University, Jining, Shandong, 272029, PR China
| | - Jingtong Wang
- Department of Emergency Medicine, Affiliated Hospital of Jining Medical University, Jining, Shandong, 272029, PR China
| | - Bin Zhang
- Department of Laboratory Medicine, Affiliated Hospital of Jining Medical University, Jining, Shandong, 272029, PR China
| | - Feng Jin
- Department of Neurosurgery, Qingdao Central Hospital, University of Health and Rehabilitation Sciences &Qingdao Central Hospital Medical Group, Qingdao, Shandong, 266042, PR China
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Deng L, Pollmeier L, Bednarz R, Cao C, Laurette P, Wirth L, Mamazhakypov A, Bode C, Hein L, Gilsbach R, Lother A. Atlas of cardiac endothelial cell enhancer elements linking the mineralocorticoid receptor to pathological gene expression. SCIENCE ADVANCES 2024; 10:eadj5101. [PMID: 38446896 PMCID: PMC10917356 DOI: 10.1126/sciadv.adj5101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 01/31/2024] [Indexed: 03/08/2024]
Abstract
Endothelial cells play crucial roles in physiology and are increasingly recognized as therapeutic targets in cardiovascular disease. Here, we analyzed the regulatory landscape of cardiac endothelial cells by assessing chromatin accessibility, histone modifications, and 3D chromatin organization and confirmed the functional relevance of enhancer-promoter interactions by CRISPRi-mediated enhancer silencing. We used this dataset to explore mechanisms of transcriptional regulation in cardiovascular disease and compared six different experimental models of heart failure, hypertension, or diabetes. Enhancers that regulate gene expression in diseased endothelial cells were enriched with binding sites for a distinct set of transcription factors, including the mineralocorticoid receptor (MR), a known drug target in heart failure and hypertension. For proof of concept, we applied endothelial cell-specific MR deletion in mice to confirm MR-dependent gene expression and predicted direct MR target genes. Overall, we have compiled here a comprehensive atlas of cardiac endothelial cell enhancer elements that provides insight into the role of transcription factors in cardiovascular disease.
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Affiliation(s)
- Lisa Deng
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), Cardiovascular Research Track, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Luisa Pollmeier
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Rebecca Bednarz
- Institute of Experimental Cardiology, Heidelberg University Hospital, Heidelberg, Germany
- DZHK (German Center of Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Can Cao
- Institute of Experimental Cardiology, Heidelberg University Hospital, Heidelberg, Germany
- DZHK (German Center of Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Patrick Laurette
- Institute of Experimental Cardiology, Heidelberg University Hospital, Heidelberg, Germany
- DZHK (German Center of Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Luisa Wirth
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Argen Mamazhakypov
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Christine Bode
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Lutz Hein
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
| | - Ralf Gilsbach
- Institute of Experimental Cardiology, Heidelberg University Hospital, Heidelberg, Germany
- DZHK (German Center of Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Achim Lother
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Interdisciplinary Medical Intensive Care, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
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Li J, Zhu J, Gray O, Sobreira DR, Wu D, Huang RT, Miao B, Sakabe NJ, Krause MD, Kaikkonen MU, Romanoski CE, Nobrega MA, Fang Y. Mechanosensitive super-enhancers regulate genes linked to atherosclerosis in endothelial cells. J Cell Biol 2024; 223:e202211125. [PMID: 38231044 PMCID: PMC10794123 DOI: 10.1083/jcb.202211125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 10/05/2023] [Accepted: 12/21/2023] [Indexed: 01/18/2024] Open
Abstract
Vascular homeostasis and pathophysiology are tightly regulated by mechanical forces generated by hemodynamics. Vascular disorders such as atherosclerotic diseases largely occur at curvatures and bifurcations where disturbed blood flow activates endothelial cells while unidirectional flow at the straight part of vessels promotes endothelial health. Integrated analysis of the endothelial transcriptome, the 3D epigenome, and human genetics systematically identified the SNP-enriched cistrome in vascular endothelium subjected to well-defined atherosclerosis-prone disturbed flow or atherosclerosis-protective unidirectional flow. Our results characterized the endothelial typical- and super-enhancers and underscored the critical regulatory role of flow-sensitive endothelial super-enhancers. CRISPR interference and activation validated the function of a previously unrecognized unidirectional flow-induced super-enhancer that upregulates antioxidant genes NQO1, CYB5B, and WWP2, and a disturbed flow-induced super-enhancer in endothelium which drives prothrombotic genes EDN1 and HIVEP in vascular endothelium. Our results employing multiomics identify the cis-regulatory architecture of the flow-sensitive endothelial epigenome related to atherosclerosis and highlight the regulatory role of super-enhancers in mechanotransduction mechanisms.
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Affiliation(s)
- Jin Li
- Committee on Molecular Metabolism and Nutrition, Biological Sciences Division, The University of Chicago, Chicago, IL, USA
- Department of Medicine, Biological Sciences Division, The University of Chicago, Chicago, IL, USA
| | - Jiayu Zhu
- Department of Medicine, Biological Sciences Division, The University of Chicago, Chicago, IL, USA
| | - Olivia Gray
- Department of Human Genetics, Biological Sciences Division, The University of Chicago, Chicago, IL, USA
| | - Débora R. Sobreira
- Department of Human Genetics, Biological Sciences Division, The University of Chicago, Chicago, IL, USA
| | - David Wu
- Committee on Molecular Metabolism and Nutrition, Biological Sciences Division, The University of Chicago, Chicago, IL, USA
- Department of Medicine, Biological Sciences Division, The University of Chicago, Chicago, IL, USA
| | - Ru-Ting Huang
- Department of Medicine, Biological Sciences Division, The University of Chicago, Chicago, IL, USA
| | - Bernadette Miao
- Department of Medicine, Biological Sciences Division, The University of Chicago, Chicago, IL, USA
| | - Noboru J. Sakabe
- Department of Human Genetics, Biological Sciences Division, The University of Chicago, Chicago, IL, USA
| | - Matthew D. Krause
- Department of Medicine, Biological Sciences Division, The University of Chicago, Chicago, IL, USA
| | - Minna U. Kaikkonen
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Casey E. Romanoski
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA
| | - Marcelo A. Nobrega
- Department of Human Genetics, Biological Sciences Division, The University of Chicago, Chicago, IL, USA
| | - Yun Fang
- Committee on Molecular Metabolism and Nutrition, Biological Sciences Division, The University of Chicago, Chicago, IL, USA
- Department of Medicine, Biological Sciences Division, The University of Chicago, Chicago, IL, USA
- Committee on Molecular Medicine, The University of Chicago, Chicago, IL, USA
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8
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Payne S, Neal A, De Val S. Transcription factors regulating vasculogenesis and angiogenesis. Dev Dyn 2024; 253:28-58. [PMID: 36795082 PMCID: PMC10952167 DOI: 10.1002/dvdy.575] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 02/06/2023] [Accepted: 02/06/2023] [Indexed: 02/17/2023] Open
Abstract
Transcription factors (TFs) play a crucial role in regulating the dynamic and precise patterns of gene expression required for the initial specification of endothelial cells (ECs), and during endothelial growth and differentiation. While sharing many core features, ECs can be highly heterogeneous. Differential gene expression between ECs is essential to pattern the hierarchical vascular network into arteries, veins and capillaries, to drive angiogenic growth of new vessels, and to direct specialization in response to local signals. Unlike many other cell types, ECs have no single master regulator, instead relying on differing combinations of a necessarily limited repertoire of TFs to achieve tight spatial and temporal activation and repression of gene expression. Here, we will discuss the cohort of TFs known to be involved in directing gene expression during different stages of mammalian vasculogenesis and angiogenesis, with a primary focus on development.
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Affiliation(s)
- Sophie Payne
- Department of Physiology, Anatomy and GeneticsInstitute of Developmental and Regenerative Medicine, University of OxfordOxfordUK
| | - Alice Neal
- Department of Physiology, Anatomy and GeneticsInstitute of Developmental and Regenerative Medicine, University of OxfordOxfordUK
| | - Sarah De Val
- Department of Physiology, Anatomy and GeneticsInstitute of Developmental and Regenerative Medicine, University of OxfordOxfordUK
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Zhang J, Zhang S, Xu S, Zhu Z, Li J, Wang Z, Wada Y, Gatt A, Liu J. Oxidative Stress Induces E-Selectin Expression through Repression of Endothelial Transcription Factor ERG. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:1835-1843. [PMID: 37930129 PMCID: PMC10694031 DOI: 10.4049/jimmunol.2300043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 10/12/2023] [Indexed: 11/07/2023]
Abstract
Oxidative stress induces a prothrombotic state through enhancement of adhesion properties of the endothelium. E-selectin, an endothelial cell adhesion molecule, becomes a therapeutic target for venous thrombosis, whereas the regulatory mechanisms of its expression have not been fully understood. In the present study, we report that H2O2 treatment increases expression of E-selectin but decreases expression of the endothelial transcription factor ETS-related gene (ERG) in HUVECs in a dose- and time-dependent manner. In BALB/c mice treated with hypochlorous acid, E-selectin expression is increased and ERG expression is decreased in endothelial cells of the brain and lung. RNA interference of ERG upregulates E-selectin expression, whereas transfection of ERG-expressing plasmid downregulates E-selectin expression in HUVECs. Knockdown or overexpression of ERG comprises H2O2-induced E-selectin expression in HUVECs. Deletion of the Erg gene in mice results in embryonic lethality at embryonic days 10.5-12.5, and E-selectin expression is increased in the Erg-/- embryos. No chromatin loop was found on the E-selectin gene or its promoter region by capture high-throughput chromosome conformation capture. Chromatin immunoprecipitation and luciferase reporter assay determined that the -127 ERG binding motif mediates ERG-repressed E-selectin promoter activity. In addition, ERG decreases H2O2-induced monocyte adhesion. Together, ERG represses the E-selectin gene transcription and inhibits oxidative stress-induced endothelial cell adhesion.
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Affiliation(s)
- Jinjin Zhang
- Medical Research Center, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, China
| | - Shuo Zhang
- Medical Research Center, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, China
| | - Shanhu Xu
- Medical Research Center, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, China
| | - Zhiying Zhu
- Medical Research Center, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, China
| | - Jiang Li
- Medical Research Center, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, China
| | - Zengjin Wang
- Institute of Microvascular Medicine, Medical Research Center, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, China
| | - Youichiro Wada
- Isotope Science Center, The University of Tokyo, Tokyo, Japan
| | - Alex Gatt
- Department of Pathology, Faculty of Medicine and Surgery, University of Malta, Tal-Qroqq, Msida, Malta
- Hematology Laboratory, Department of Pathology, Mater Dei Hospital, Msida, Malta
| | - Ju Liu
- Medical Research Center, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, China
- Institute of Microvascular Medicine, Medical Research Center, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, China
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10
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Armstrong ND, Srinivasasainagendra V, Ammous F, Assimes TL, Beitelshees AL, Brody J, Cade BE, Ida Chen YD, Chen H, de Vries PS, Floyd JS, Franceschini N, Guo X, Hellwege JN, House JS, Hwu CM, Kardia SLR, Lange EM, Lange LA, McDonough CW, Montasser ME, O’Connell JR, Shuey MM, Sun X, Tanner RM, Wang Z, Zhao W, Carson AP, Edwards TL, Kelly TN, Kenny EE, Kooperberg C, Loos RJF, Morrison AC, Motsinger-Reif A, Psaty BM, Rao DC, Redline S, Rich SS, Rotter JI, Smith JA, Smith AV, Irvin MR, Arnett DK. Whole genome sequence analysis of apparent treatment resistant hypertension status in participants from the Trans-Omics for Precision Medicine program. Front Genet 2023; 14:1278215. [PMID: 38162683 PMCID: PMC10755672 DOI: 10.3389/fgene.2023.1278215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 11/24/2023] [Indexed: 01/03/2024] Open
Abstract
Introduction: Apparent treatment-resistant hypertension (aTRH) is characterized by the use of four or more antihypertensive (AHT) classes to achieve blood pressure (BP) control. In the current study, we conducted single-variant and gene-based analyses of aTRH among individuals from 12 Trans-Omics for Precision Medicine cohorts with whole-genome sequencing data. Methods: Cases were defined as individuals treated for hypertension (HTN) taking three different AHT classes, with average systolic BP ≥ 140 or diastolic BP ≥ 90 mmHg, or four or more medications regardless of BP (n = 1,705). A normotensive control group was defined as individuals with BP < 140/90 mmHg (n = 22,079), not on AHT medication. A second control group comprised individuals who were treatment responsive on one AHT medication with BP < 140/ 90 mmHg (n = 5,424). Logistic regression with kinship adjustment using the Scalable and Accurate Implementation of Generalized mixed models (SAIGE) was performed, adjusting for age, sex, and genetic ancestry. We assessed variants using SKAT-O in rare-variant analyses. Single-variant and gene-based tests were conducted in a pooled multi-ethnicity stratum, as well as self-reported ethnic/racial strata (European and African American). Results: One variant in the known HTN locus, KCNK3, was a top finding in the multi-ethnic analysis (p = 8.23E-07) for the normotensive control group [rs12476527, odds ratio (95% confidence interval) = 0.80 (0.74-0.88)]. This variant was replicated in the Vanderbilt University Medical Center's DNA repository data. Aggregate gene-based signals included the genes AGTPBP, MYL4, PDCD4, BBS9, ERG, and IER3. Discussion: Additional work validating these loci in larger, more diverse populations, is warranted to determine whether these regions influence the pathobiology of aTRH.
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Affiliation(s)
- Nicole D. Armstrong
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | | | - Farah Ammous
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, United States
- Survey Research Center, Institute for Social Research, Ann Arbor, MI, United States
| | - Themistocles L. Assimes
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Amber L. Beitelshees
- Division of Endocrinology, Diabetes, and Nutrition, Program for Personalized and Genomic Medicine, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Jennifer Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, United States
| | - Brian E. Cade
- Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, United States
| | - Han Chen
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, United States
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Paul S. de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - James S. Floyd
- Department of Medicine, University of Washington, Seattle, WA, United States
- Department of Epidemiology, University of Washington, Seattle, WA, United States
| | - Nora Franceschini
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, United States
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, United States
| | - Jacklyn N. Hellwege
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, United States
| | - John S. House
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, United States
| | - Chii-Min Hwu
- Section of Endocrinology and Metabolism, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Sharon L. R. Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - Ethan M. Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Leslie A. Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Caitrin W. McDonough
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, FL, United States
| | - May E. Montasser
- Division of Endocrinology, Diabetes, and Nutrition, Program for Personalized and Genomic Medicine, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | | | - Megan M. Shuey
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Xiao Sun
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, United States
| | - Rikki M. Tanner
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Zhe Wang
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, United States
- Survey Research Center, Institute for Social Research, Ann Arbor, MI, United States
| | - April P. Carson
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, United States
| | - Todd L. Edwards
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, United States
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Tanika N. Kelly
- Division of Nephrology, Department of Medicine, College of Medicine, University of Illinois Chicago, Chicago, IL, United States
| | - Eimear E. Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Ruth J. F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Alanna C. Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Alison Motsinger-Reif
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, United States
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, United States
- Department of Medicine, University of Washington, Seattle, WA, United States
- Department of Epidemiology, University of Washington, Seattle, WA, United States
| | - Dabeeru C. Rao
- Division of Biostatistics, School of Medicine, Washington University in St. Louis, St. Louis, MO, United States
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - Stephen S. Rich
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, United States
| | - Jennifer A. Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, United States
- Survey Research Center, Institute for Social Research, Ann Arbor, MI, United States
| | - Albert V. Smith
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Marguerite R. Irvin
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Donna K. Arnett
- Office of the Provost, University of South Carolina, Columbia, SC, United States
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11
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Searcy MB, Larsen RK, Stevens BT, Zhang Y, Jin H, Drummond CJ, Langdon CG, Gadek KE, Vuong K, Reed KB, Garcia MR, Xu B, Kimbrough DW, Adkins GE, Djekidel N, Porter SN, Schreiner PA, Pruett-Miller SM, Abraham BJ, Rehg JE, Hatley ME. PAX3-FOXO1 dictates myogenic reprogramming and rhabdomyosarcoma identity in endothelial progenitors. Nat Commun 2023; 14:7291. [PMID: 37968277 PMCID: PMC10651858 DOI: 10.1038/s41467-023-43044-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 10/27/2023] [Indexed: 11/17/2023] Open
Abstract
Fusion-positive rhabdomyosarcoma (FP-RMS) driven by the expression of the PAX3-FOXO1 (P3F) fusion oncoprotein is an aggressive subtype of pediatric rhabdomyosarcoma. FP-RMS histologically resembles developing muscle yet occurs throughout the body in areas devoid of skeletal muscle highlighting that FP-RMS is not derived from an exclusively myogenic cell of origin. Here we demonstrate that P3F reprograms mouse and human endothelial progenitors to FP-RMS. We show that P3F expression in aP2-Cre expressing cells reprograms endothelial progenitors to functional myogenic stem cells capable of regenerating injured muscle fibers. Further, we describe a FP-RMS mouse model driven by P3F expression and Cdkn2a loss in endothelial cells. Additionally, we show that P3F expression in TP53-null human iPSCs blocks endothelial-directed differentiation and guides cells to become myogenic cells that form FP-RMS tumors in immunocompromised mice. Together these findings demonstrate that FP-RMS can originate from aberrant development of non-myogenic cells driven by P3F.
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Affiliation(s)
- Madeline B Searcy
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- St. Jude Graduate School of Biomedical Sciences, Memphis, TN, 38105, USA
| | - Randolph K Larsen
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- St. Jude Graduate School of Biomedical Sciences, Memphis, TN, 38105, USA
| | - Bradley T Stevens
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- St. Jude Graduate School of Biomedical Sciences, Memphis, TN, 38105, USA
| | - Yang Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Hongjian Jin
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Catherine J Drummond
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Casey G Langdon
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Katherine E Gadek
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Kyna Vuong
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Kristin B Reed
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Matthew R Garcia
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Darden W Kimbrough
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Rhodes College, Memphis, TN, 38112, USA
| | - Grace E Adkins
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- St. Jude Graduate School of Biomedical Sciences, Memphis, TN, 38105, USA
| | - Nadhir Djekidel
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Shaina N Porter
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Patrick A Schreiner
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Shondra M Pruett-Miller
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Brian J Abraham
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jerold E Rehg
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Mark E Hatley
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
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12
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Randi AM, Jones D, Peghaire C, Arachchillage DJ. Mechanisms regulating heterogeneity of hemostatic gene expression in endothelial cells. J Thromb Haemost 2023; 21:3056-3066. [PMID: 37393001 DOI: 10.1016/j.jtha.2023.06.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 05/30/2023] [Accepted: 06/20/2023] [Indexed: 07/03/2023]
Abstract
The hemostatic system involves an array of circulating coagulation factors that work in concert with platelets and the vascular endothelium to promote clotting in a space- and time-defined manner. Despite equal systemic exposure to circulating factors, bleeding and thrombotic diseases tend to prefer specific sites, suggesting an important role for local factors. This may be provided by endothelial heterogeneity. Endothelial cells differ not only between arteries, veins, and capillaries but also between microvascular beds from different organs, which present unique organotypic morphology and functional and molecular profiles. Accordingly, regulators of hemostasis are not uniformly distributed in the vasculature. The establishment and maintenance of endothelial diversity are orchestrated at the transcriptional level. Recent transcriptomic and epigenomic studies have provided a global picture of endothelial cell heterogeneity. In this review, we discuss the organotypic differences in the hemostatic profile of endothelial cells; we focus on 2 major endothelial regulators of hemostasis, namely von Willebrand factor and thrombomodulin, to provide examples of transcriptional mechanisms that control heterogeneity; finally, we consider some of the methodological challenges and opportunities for future studies.
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Affiliation(s)
- Anna M Randi
- National Heart and Lung Institute, Imperial College London, London, UK.
| | - Daisy Jones
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Claire Peghaire
- University of Bordeaux, Unité Mixte de Recherche-1034 INSERM, Biology of Cardiovascular Diseases, Pessac, France
| | - Deepa J Arachchillage
- Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, UK; Department of Haematology, Imperial College Healthcare NHS Trust, London, UK. https://twitter.com/DeepaArachchil1
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13
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Kaur L, Sundrani D, Dave K, Randhir K, Mehendale S, Bayyana S, Kalyanaraman K, Chandak GR, Joshi S. Hypoxia Inducible Factors (HIF1α and HIF3α) are differentially methylated in preeclampsia placentae and are associated with birth outcomes. Mol Cell Biochem 2023; 478:2309-2318. [PMID: 36708442 DOI: 10.1007/s11010-023-04661-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/09/2023] [Indexed: 01/29/2023]
Abstract
Preeclampsia is a placental vascular pathology and hypoxia is known to influence placental angiogenesis. Hypoxia Inducible Factors (HIF1α and HIF3α) mediate the response to cellular oxygen concentration and bind to hypoxia response element of target genes. However the mechanism regulating above activity is not well-understood. We investigated if placental DNA methylation (DNAm) and expression of HIF1α and 3α genes are altered and associated with pre-eclampsia, placental weight and birth outcomes. Using a cohort comprising women with preeclampsia [N = 100, delivering at term (N = 43) and preterm (N = 57)] and normotensive controls (N = 100), we analysed DNAm in HIF1α and 3α, and their mRNA expression in placentae, employing pyrosequencing and quantitative real-time PCR, respectively. We observed significant hypermethylation at cg22891070 of HIF3α in preeclampsia placentae compared to controls (β = 1.5%, p = 0.04). CpG8 in the promoter region of HIF1α, showed marginally significant hypomethylation in preterm preeclampsia compared to controls (β = - 0.15%, p = 0.055). HIF1α expression was significantly lower in preterm preeclampsia compared to controls (mean ± SE = 10.16 ± 2.00 vs 4.25 ± 0.90, p = 0.04). Further, DNAm in HIF1α promoter region was negatively associated with its expression levels (β = - 0.165, p = 0.024). Several CpGs in HIF1α were negatively associated with placental weight and birth outcomes including birth weight (β range = - 0.224-0.300) and birth length [β range = - 0.248 to - 0.301 (p < 0.05 for all)]. Overall, we demonstrate altered DNAm in HIF1α and HIF3α in preeclampsia placentae, also associated with various birth outcomes. Correlation of DNAm in HIF1α and its expression suggests a possible role in the pathogenesis of pre-eclampsia. Further investigations on interactions between HIF1α and HIF3α in preeclampsia would be interesting.
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Affiliation(s)
- Lovejeet Kaur
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, 500007, India
- Maternal and Child Health (MCH), Translational Health Science and Technology Institute (THSTI), Faridabad, 121001, India
| | - Deepali Sundrani
- Mother and Child Health, Interactive Research School for Health Affairs (IRSHA), Bharati Vidyapeeth (Deemed to be) University, Pune Satara Road, Pune, 411043, India
| | - Kinjal Dave
- Mother and Child Health, Interactive Research School for Health Affairs (IRSHA), Bharati Vidyapeeth (Deemed to be) University, Pune Satara Road, Pune, 411043, India
| | - Karuna Randhir
- Mother and Child Health, Interactive Research School for Health Affairs (IRSHA), Bharati Vidyapeeth (Deemed to be) University, Pune Satara Road, Pune, 411043, India
| | - Savita Mehendale
- Department of Gynecology and Obstetrics, Bharati Vidyapeeth Medical College and Hospital, Pune, 411043, India
| | - Swati Bayyana
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, 500007, India
| | - Kumaran Kalyanaraman
- CSI Epidemiology Research Unit, Holdsworth Memorial Hospital, Mysore, India
- MRC Lifecourse Epidemiology Centre, University of Southampton, Southampton, UK
| | - Giriraj R Chandak
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, 500007, India.
| | - Sadhana Joshi
- Mother and Child Health, Interactive Research School for Health Affairs (IRSHA), Bharati Vidyapeeth (Deemed to be) University, Pune Satara Road, Pune, 411043, India.
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14
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Deng Z, Rong S, Gan L, Wang F, Bao L, Cai F, Liao Z, Jin Y, Feng S, Feng Z, Wei Y, Chen R, Jin Y, Zhou Y, Zheng X, Huang L, Zhao L. Temporal transcriptome features identify early skeletal commitment during human epiphysis development at single-cell resolution. iScience 2023; 26:107200. [PMID: 37554462 PMCID: PMC10405011 DOI: 10.1016/j.isci.2023.107200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 05/18/2023] [Accepted: 06/20/2023] [Indexed: 08/10/2023] Open
Abstract
Human epiphyseal development has been mainly investigated through radiological and histological approaches, uncovering few details of cellular temporal genetic alternations. Using single-cell RNA sequencing, we investigated the dynamic transcriptome changes during post-conception weeks (PCWs) 15-25 of human distal femoral epiphysis cells. We find epiphyseal cells contain multiple subtypes distinguished by specific markers, gene signatures, Gene Ontology (GO) enrichment analysis, and gene set variation analysis (GSVA). We identify the populations committed to cartilage or ossification at this time, although the secondary ossification centers (SOCs) have not formed. We describe the temporal alternation in transcriptional expression utilizing trajectories, transcriptional regulatory networks, and intercellular communication analyses. Moreover, we find the emergence of the ossification-committed population is correlated with the COL2A1-(ITGA2/11+ITGB1) signaling. NOTCH signaling may contribute to the formation of cartilage canals and ossification via NOTCH signaling. Our findings will advance the understanding of single-cell genetic changes underlying fetal epiphysis development.
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Affiliation(s)
- Zhonghao Deng
- Department of Orthopaedic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Shengwei Rong
- Department of Orthopaedic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Lu Gan
- Department of Orthopaedic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Fuhua Wang
- Department of Orthopaedic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Liangxiao Bao
- Department of Orthopaedic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Fang Cai
- Department of Obstetrics and Gynecology, Southern Medical University Nanfang Hospital Taihe Branch, Guangzhou, Guangdong 510515, China
| | - Zheting Liao
- Department of Orthopaedic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Yu Jin
- Department of Orthopaedic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Shuhao Feng
- Department of Orthopaedic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Zihang Feng
- Department of Orthopaedic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Yiran Wei
- Department of Orthopaedic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Ruge Chen
- Department of Orthopaedic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Yangchen Jin
- Department of Orthopaedic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Yanli Zhou
- Department of Obstetrics and Gynecology, Southern Medical University Nanfang Hospital, Guangzhou, Guangdong 510515, China
| | - Xiaoyong Zheng
- Orthopaedic Department, The 8th medical center of Chinese PLA General Hospital, Beijing 100091, China
| | - Liping Huang
- Department of Obstetrics and Gynecology, Southern Medical University Nanfang Hospital, Guangzhou, Guangdong 510515, China
| | - Liang Zhao
- Department of Orthopaedic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong 510515, China
- Department of Orthopaedic Surgery, Shunde First People Hospital, Foshan, Guangdong 528300, China
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15
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Zerella JR, Homan CC, Arts P, Brown AL, Scott HS, Hahn CN. Transcription factor genetics and biology in predisposition to bone marrow failure and hematological malignancy. Front Oncol 2023; 13:1183318. [PMID: 37377909 PMCID: PMC10291195 DOI: 10.3389/fonc.2023.1183318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
Transcription factors (TFs) play a critical role as key mediators of a multitude of developmental pathways, with highly regulated and tightly organized networks crucial for determining both the timing and pattern of tissue development. TFs can act as master regulators of both primitive and definitive hematopoiesis, tightly controlling the behavior of hematopoietic stem and progenitor cells (HSPCs). These networks control the functional regulation of HSPCs including self-renewal, proliferation, and differentiation dynamics, which are essential to normal hematopoiesis. Defining the key players and dynamics of these hematopoietic transcriptional networks is essential to understanding both normal hematopoiesis and how genetic aberrations in TFs and their networks can predispose to hematopoietic disease including bone marrow failure (BMF) and hematological malignancy (HM). Despite their multifaceted and complex involvement in hematological development, advances in genetic screening along with elegant multi-omics and model system studies are shedding light on how hematopoietic TFs interact and network to achieve normal cell fates and their role in disease etiology. This review focuses on TFs which predispose to BMF and HM, identifies potential novel candidate predisposing TF genes, and examines putative biological mechanisms leading to these phenotypes. A better understanding of the genetics and molecular biology of hematopoietic TFs, as well as identifying novel genes and genetic variants predisposing to BMF and HM, will accelerate the development of preventative strategies, improve clinical management and counseling, and help define targeted treatments for these diseases.
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Affiliation(s)
- Jiarna R. Zerella
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
| | - Claire C. Homan
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
| | - Peer Arts
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
| | - Anna L. Brown
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
| | - Hamish S. Scott
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
| | - Christopher N. Hahn
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
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16
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Walters R, Vasilaki E, Aman J, Chen CN, Wu Y, Liang OD, Ashek A, Dubois O, Zhao L, Sabrin F, Cebola I, Ferrer J, Morrell NW, Klinger JR, Wilkins MR, Zhao L, Rhodes CJ. SOX17 Enhancer Variants Disrupt Transcription Factor Binding And Enhancer Inactivity Drives Pulmonary Hypertension. Circulation 2023; 147:1606-1621. [PMID: 37066790 PMCID: PMC7614572 DOI: 10.1161/circulationaha.122.061940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 03/15/2023] [Indexed: 04/18/2023]
Abstract
BACKGROUND Pulmonary arterial hypertension (PAH) is a rare disease characterized by remodeling of the pulmonary arteries, increased vascular resistance, and right-sided heart failure. Genome-wide association studies of idiopathic/heritable PAH established novel genetic risk variants, including conserved enhancers upstream of transcription factor (TF) SOX17 containing 2 independent signals. SOX17 is an important TF in embryonic development and in the homeostasis of pulmonary artery endothelial cells (hPAEC) in the adult. Rare pathogenic mutations in SOX17 cause heritable PAH. We hypothesized that PAH risk alleles in an enhancer region impair TF-binding upstream of SOX17, which in turn reduces SOX17 expression and contributes to disturbed endothelial cell function and PAH development. METHODS CRISPR manipulation and siRNA were used to modulate SOX17 expression. Electromobility shift assays were used to confirm in silico-predicted TF differential binding to the SOX17 variants. Functional assays in hPAECs were used to establish the biological consequences of SOX17 loss. In silico analysis with the connectivity map was used to predict compounds that rescue disturbed SOX17 signaling. Mice with deletion of the SOX17-signal 1 enhancer region (SOX17-4593/enhKO) were phenotyped in response to chronic hypoxia and SU5416/hypoxia. RESULTS CRISPR inhibition of SOX17-signal 2 and deletion of SOX17-signal 1 specifically decreased SOX17 expression. Electromobility shift assays demonstrated differential binding of hPAEC nuclear proteins to the risk and nonrisk alleles from both SOX17 signals. Candidate TFs HOXA5 and ROR-α were identified through in silico analysis and antibody electromobility shift assays. Analysis of the hPAEC transcriptomes revealed alteration of PAH-relevant pathways on SOX17 silencing, including extracellular matrix regulation. SOX17 silencing in hPAECs resulted in increased apoptosis, proliferation, and disturbance of barrier function. With the use of the connectivity map, compounds were identified that reversed the SOX17-dysfunction transcriptomic signatures in hPAECs. SOX17 enhancer knockout in mice reduced lung SOX17 expression, resulting in more severe pulmonary vascular leak and hypoxia or SU5416/hypoxia-induced pulmonary hypertension. CONCLUSIONS Common PAH risk variants upstream of the SOX17 promoter reduce endothelial SOX17 expression, at least in part, through differential binding of HOXA5 and ROR-α. Reduced SOX17 expression results in disturbed hPAEC function and PAH. Existing drug compounds can reverse the disturbed SOX17 pulmonary endothelial transcriptomic signature.
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Affiliation(s)
- Rachel Walters
- National Heart and Lung Institute, Hammersmith Hospital, Imperial College, London, United Kingdom (R.W., E.V., J.A., C.-N.C., Y.W., A.A., O.D., L.Z., F.S., M.R.W., L.Z., C.J.R.)
| | - Eleni Vasilaki
- National Heart and Lung Institute, Hammersmith Hospital, Imperial College, London, United Kingdom (R.W., E.V., J.A., C.-N.C., Y.W., A.A., O.D., L.Z., F.S., M.R.W., L.Z., C.J.R.)
| | - Jurjan Aman
- National Heart and Lung Institute, Hammersmith Hospital, Imperial College, London, United Kingdom (R.W., E.V., J.A., C.-N.C., Y.W., A.A., O.D., L.Z., F.S., M.R.W., L.Z., C.J.R.)
- Department of Pulmonary Medicine, Amsterdam University Medical Center, The Netherlands (J.A.)
| | - Chien-Nien Chen
- National Heart and Lung Institute, Hammersmith Hospital, Imperial College, London, United Kingdom (R.W., E.V., J.A., C.-N.C., Y.W., A.A., O.D., L.Z., F.S., M.R.W., L.Z., C.J.R.)
| | - Yukyee Wu
- National Heart and Lung Institute, Hammersmith Hospital, Imperial College, London, United Kingdom (R.W., E.V., J.A., C.-N.C., Y.W., A.A., O.D., L.Z., F.S., M.R.W., L.Z., C.J.R.)
| | - Olin D Liang
- Division of Hematology/Oncology, Department of Medicine (O.D.L.), Rhode Island Hospital and Warren Alpert Medical School of Brown University, Providence
| | - Ali Ashek
- National Heart and Lung Institute, Hammersmith Hospital, Imperial College, London, United Kingdom (R.W., E.V., J.A., C.-N.C., Y.W., A.A., O.D., L.Z., F.S., M.R.W., L.Z., C.J.R.)
| | - Olivier Dubois
- National Heart and Lung Institute, Hammersmith Hospital, Imperial College, London, United Kingdom (R.W., E.V., J.A., C.-N.C., Y.W., A.A., O.D., L.Z., F.S., M.R.W., L.Z., C.J.R.)
| | - Lin Zhao
- National Heart and Lung Institute, Hammersmith Hospital, Imperial College, London, United Kingdom (R.W., E.V., J.A., C.-N.C., Y.W., A.A., O.D., L.Z., F.S., M.R.W., L.Z., C.J.R.)
| | - Farah Sabrin
- National Heart and Lung Institute, Hammersmith Hospital, Imperial College, London, United Kingdom (R.W., E.V., J.A., C.-N.C., Y.W., A.A., O.D., L.Z., F.S., M.R.W., L.Z., C.J.R.)
| | - Inês Cebola
- Section of Genetics & Genomics, Department of Metabolism, Digestion & Reproduction, Hammersmith Hospital, Imperial College, London, United Kingdom (I.C., J.F.)
| | - Jorge Ferrer
- Section of Genetics & Genomics, Department of Metabolism, Digestion & Reproduction, Hammersmith Hospital, Imperial College, London, United Kingdom (I.C., J.F.)
- Computational Biology and Health Genomics Programme, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Spain (J.F.)
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas, Barcelona, Spain (J.F.)
| | - Nicholas W Morrell
- Department of Medicine, University of Cambridge, United Kingdom (N.W.M.)
- NIHR BioResource for Translational Research, University of Cambridge, United Kingdom (N.W.M.)
- On Behalf of the British Heart Foundation/Medical Research Council UK PAH Cohort Consortium (N.W.M., M.R.W., C.J.R.)
| | - James R Klinger
- Division of Pulmonary, Sleep and Critical Care Medicine, Department of Medicine (J.R.K.), Rhode Island Hospital and Warren Alpert Medical School of Brown University, Providence
| | - Martin R Wilkins
- National Heart and Lung Institute, Hammersmith Hospital, Imperial College, London, United Kingdom (R.W., E.V., J.A., C.-N.C., Y.W., A.A., O.D., L.Z., F.S., M.R.W., L.Z., C.J.R.)
- On Behalf of the British Heart Foundation/Medical Research Council UK PAH Cohort Consortium (N.W.M., M.R.W., C.J.R.)
| | - Lan Zhao
- National Heart and Lung Institute, Hammersmith Hospital, Imperial College, London, United Kingdom (R.W., E.V., J.A., C.-N.C., Y.W., A.A., O.D., L.Z., F.S., M.R.W., L.Z., C.J.R.)
| | - Christopher J Rhodes
- National Heart and Lung Institute, Hammersmith Hospital, Imperial College, London, United Kingdom (R.W., E.V., J.A., C.-N.C., Y.W., A.A., O.D., L.Z., F.S., M.R.W., L.Z., C.J.R.)
- On Behalf of the British Heart Foundation/Medical Research Council UK PAH Cohort Consortium (N.W.M., M.R.W., C.J.R.)
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17
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Yang Z, Zheng Y, Wu H, Xie H, Zhao J, Chen Z, Li L, Yue X, Zhao B, Bian E. Integrative analysis of a novel super-enhancer-associated lncRNA prognostic signature and identifying LINC00945 in aggravating glioma progression. Hum Genomics 2023; 17:33. [PMID: 37004060 PMCID: PMC10064652 DOI: 10.1186/s40246-023-00480-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 03/25/2023] [Indexed: 04/03/2023] Open
Abstract
BACKGROUND Super-enhancers (SEs), driving high-level expression of genes with tumor-promoting functions, have been investigated recently. However, the roles of super-enhancer-associated lncRNAs (SE-lncRNAs) in tumors remain undetermined, especially in gliomas. We here established a SE-lncRNAs expression-based prognostic signature to choose the effective treatment of glioma and identify a novel therapeutic target. METHODS Combined analysis of RNA sequencing (RNA-seq) data and ChIP sequencing (ChIP-seq) data of glioma patient-derived glioma stem cells (GSCs) screened SE-lncRNAs. Chinese Glioma Genome Atlas (CGGA) and The Cancer Genome Atlas (TCGA) datasets served to construct and validate SE-lncRNA prognostic signature. The immune profiles and potential immuno- and chemotherapies response prediction value of the signature were also explored. Moreover, we verified the epigenetic activation mechanism of LINC00945 via the ChIP assay, and its effect on glioma was determined by performing the functional assay and a mouse xenograft model. RESULTS 6 SE-lncRNAs were obtained and identified three subgroups of glioma patients with different prognostic and clinical features. A risk signature was further constructed and demonstrated to be an independent prognostic factor. The high-risk group exhibited an immunosuppressive microenvironment and was higher enrichment of M2 macrophage, regulatory T cells (Tregs), and Cancer-associated fibroblasts (CAFs). Patients in the high-risk group were better candidates for immunotherapy and chemotherapeutics. The SE of LINC00945 was further verified via ChIP assay. Mechanistically, BRD4 may mediate epigenetic activation of LINC00945. Additionally, overexpression of LINC00945 promoted glioma cell proliferation, EMT, migration, and invasion in vitro and xenograft tumor formation in vivo. CONCLUSION Our study constructed the first prognostic SE-lncRNA signature with the ability to optimize the choice of patients receiving immuno- and chemotherapies and provided a potential therapeutic target for glioma.
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Affiliation(s)
- Zhihao Yang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
| | - Yinfei Zheng
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
| | - Haoyuan Wu
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
| | - Han Xie
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
| | - Jiajia Zhao
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
| | - Zhigang Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
| | - Lianxin Li
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
| | - Xiaoyu Yue
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
| | - Bing Zhao
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China.
- Cerebral Vascular Disease Research Center, Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China.
| | - Erbao Bian
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China.
- Cerebral Vascular Disease Research Center, Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China.
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18
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Greene D, Pirri D, Frudd K, Sackey E, Al-Owain M, Giese APJ, Ramzan K, Riaz S, Yamanaka I, Boeckx N, Thys C, Gelb BD, Brennan P, Hartill V, Harvengt J, Kosho T, Mansour S, Masuno M, Ohata T, Stewart H, Taibah K, Turner CLS, Imtiaz F, Riazuddin S, Morisaki T, Ostergaard P, Loeys BL, Morisaki H, Ahmed ZM, Birdsey GM, Freson K, Mumford A, Turro E. Genetic association analysis of 77,539 genomes reveals rare disease etiologies. Nat Med 2023; 29:679-688. [PMID: 36928819 PMCID: PMC10033407 DOI: 10.1038/s41591-023-02211-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 01/06/2023] [Indexed: 03/18/2023]
Abstract
The genetic etiologies of more than half of rare diseases remain unknown. Standardized genome sequencing and phenotyping of large patient cohorts provide an opportunity for discovering the unknown etiologies, but this depends on efficient and powerful analytical methods. We built a compact database, the 'Rareservoir', containing the rare variant genotypes and phenotypes of 77,539 participants sequenced by the 100,000 Genomes Project. We then used the Bayesian genetic association method BeviMed to infer associations between genes and each of 269 rare disease classes assigned by clinicians to the participants. We identified 241 known and 19 previously unidentified associations. We validated associations with ERG, PMEPA1 and GPR156 by searching for pedigrees in other cohorts and using bioinformatic and experimental approaches. We provide evidence that (1) loss-of-function variants in the Erythroblast Transformation Specific (ETS)-family transcription factor encoding gene ERG lead to primary lymphoedema, (2) truncating variants in the last exon of transforming growth factor-β regulator PMEPA1 result in Loeys-Dietz syndrome and (3) loss-of-function variants in GPR156 give rise to recessive congenital hearing impairment. The Rareservoir provides a lightweight, flexible and portable system for synthesizing the genetic and phenotypic data required to study rare disease cohorts with tens of thousands of participants.
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Affiliation(s)
- Daniel Greene
- Department of Medicine, University of Cambridge, Cambridge, UK
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniela Pirri
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Karen Frudd
- National Heart and Lung Institute, Imperial College London, London, UK
- University College London Institute of Ophthalmology, University College London, London, UK
| | - Ege Sackey
- Molecular and Clinical Sciences Institute, St. George's University of London, London, UK
| | - Mohammed Al-Owain
- Department of Medical Genomics, Centre for Genomic Medicine, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Arnaud P J Giese
- Department of Otorhinolaryngology Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Khushnooda Ramzan
- Department of Clinical Genomics, Centre for Genomic Medicine, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Sehar Riaz
- Department of Otorhinolaryngology Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD, USA
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Itaru Yamanaka
- Department of Bioscience and Genetics, National Cerebral and Cardiovascular Center, Osaka, Japan
| | - Nele Boeckx
- Center for Medical Genetics, Antwerp University Hospital/University of Antwerp, Antwerp, Belgium
| | - Chantal Thys
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, KU Leuven, Leuven, Belgium
| | - Bruce D Gelb
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Paul Brennan
- Northern Genetics Service, Newcastle upon Tyne Hospitals National Health Service Trust International Centre for Life, Newcastle upon Tyne, UK
| | - Verity Hartill
- Department of Clinical Genetics, Chapel Allerton Hospital, Leeds Teaching Hospitals National Health Service Trust, Leeds, UK
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Julie Harvengt
- Centre for Medical Genetics, Centre Hospitalier Universitaire de Liège, Liège, Belgium
| | - Tomoki Kosho
- Department of Medical Genetics, Shinshu University School of Medicine, Nagano, Japan
- Center for Medical Genetics, Shinshu University Hospital, Nagano, Japan
| | - Sahar Mansour
- Molecular and Clinical Sciences Institute, St. George's University of London, London, UK
- South West Thames Regional Genetics Service, St. George's University Hospitals National Health Service Foundation Trust, London, UK
| | - Mitsuo Masuno
- Department of Medical Genetics, Kawasaki Medical School Hospital, Okayama, Japan
| | | | - Helen Stewart
- Oxford University Hospitals National Health Service Foundation Trust, Oxford, UK
| | - Khalid Taibah
- Ear Nose and Throat Medical Centre, Riyadh, Saudi Arabia
| | - Claire L S Turner
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital, Exeter, UK
| | - Faiqa Imtiaz
- Department of Clinical Genomics, Centre for Genomic Medicine, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Saima Riazuddin
- Department of Otorhinolaryngology Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD, USA
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Takayuki Morisaki
- Department of Bioscience and Genetics, National Cerebral and Cardiovascular Center, Osaka, Japan
- Division of Molecular Pathology and Department of Internal Medicine, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Pia Ostergaard
- Molecular and Clinical Sciences Institute, St. George's University of London, London, UK
| | - Bart L Loeys
- Center for Medical Genetics, Antwerp University Hospital/University of Antwerp, Antwerp, Belgium
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Hiroko Morisaki
- Department of Bioscience and Genetics, National Cerebral and Cardiovascular Center, Osaka, Japan
- Department of Medical Genetics, Sakakibara Heart Institute, Tokyo, Japan
| | - Zubair M Ahmed
- Department of Otorhinolaryngology Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD, USA
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Graeme M Birdsey
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Kathleen Freson
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, KU Leuven, Leuven, Belgium
| | - Andrew Mumford
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
- South West National Health Service Genomic Medicine Service Alliance, Bristol, UK
| | - Ernest Turro
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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19
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Schafer CM, Martin-Almedina S, Kurylowicz K, Dufton N, Osuna-Almagro L, Wu ML, Johnson CF, Shah AV, Haskard DO, Buxton A, Willis E, Wheeler K, Turner S, Chlebicz M, Scott RP, Kovats S, Cleuren A, Birdsey GM, Randi AM, Griffin CT. Cytokine-Mediated Degradation of the Transcription Factor ERG Impacts the Pulmonary Vascular Response to Systemic Inflammatory Challenge. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.08.527788. [PMID: 36798267 PMCID: PMC9934599 DOI: 10.1101/2023.02.08.527788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Background During infectious diseases, pro-inflammatory cytokines transiently destabilize interactions between adjacent vascular endothelial cells (ECs) to facilitate the passage of immune molecules and cells into tissues. However, in the lung the resulting vascular hyperpermeability can lead to organ dysfunction. Previous work identified the transcription factor ERG as a master regulator of endothelial homeostasis. Here we investigate whether the sensitivity of pulmonary blood vessels to cytokine-induced destabilization is due to organotypic mechanisms affecting the ability of endothelial ERG to protect lung ECs from inflammatory injury. Methods Cytokine-dependent ubiquitination and proteasomal degradation of ERG was analyzed in cultured Human Umbilical Vein ECs (HUVECs). Systemic administration of TNFα or the bacterial cell wall component lipopolysaccharide (LPS) was used to cause a widespread inflammatory challenge in mice; ERG protein levels were assessed by immunoprecipitation, immunoblot, and immunofluorescence. Murine Erg deletion was genetically induced in ECs ( Erg fl/fl ;Cdh5(PAC)Cre ERT2 ), and multiple organs were analyzed by histology, immunostaining, and electron microscopy. Results In vitro, TNFα promoted the ubiquitination and degradation of ERG in HUVECs, which was blocked by the proteasomal inhibitor MG132. In vivo, systemic administration of TNFα or LPS resulted in a rapid and substantial degradation of ERG within lung ECs, but not ECs of the retina, heart, liver, or kidney. Pulmonary ERG was also downregulated in a murine model of influenza infection. Erg fl/fl ;Cdh5(PAC)-Cre ERT2 mice spontaneously recapitulated aspects of inflammatory challenges, including lung-predominant vascular hyperpermeability, immune cell recruitment, and fibrosis. These phenotypes were associated with a lung-specific decrease in the expression of Tek , a gene target of ERG previously implicated in maintaining pulmonary vascular stability during inflammation. Conclusions Collectively, our data highlight a unique role for ERG in pulmonary vascular function. We propose that cytokine-induced ERG degradation and subsequent transcriptional changes in lung ECs play critical roles in the destabilization of pulmonary blood vessels during infectious diseases.
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20
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Wang R, Xu J, Tang Y, Wang Y, Zhao J, Ding L, Peng Y, Zhang Z. Transcriptome-wide analysis reveals the coregulation of RNA-binding proteins and alternative splicing genes in the development of atherosclerosis. Sci Rep 2023; 13:1764. [PMID: 36720950 PMCID: PMC9889815 DOI: 10.1038/s41598-022-26556-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 12/16/2022] [Indexed: 02/02/2023] Open
Abstract
RNA-binding proteins (RBPs) are involved in the regulation of RNA splicing, stability, and localization. How RBPs control the development of atherosclerosis, is not fully understood. To explore the relevant RNA-binding proteins (RBPs) and alternative splicing events (ASEs) in atherosclerosis. We made a comprehensive work to integrate analyses of differentially expressed genes, including differential RBPs, and variable splicing characteristics related to different stages of atherosclerosis in dataset GSE104140. A total of 3712 differentially expressed genes (DEGs) were identified, including 2921 upregulated genes and 791 downregulated genes. Further analysis screened out 54 RBP genes, and 434 AS genes overlapped DEGs. We selected high expression ten RBP genes (SAMHD1, DDX60 L, TLR7, RBM47, MYEF2, RNASE6, PARP12, APOBEC3G, SMAD9, and RNASE1) for co-expression analysis. Meanwhile, we found seven regulated alternative splicing genes (RASGs) (ABI1, FXR1, CHID1, PLEC, PRKACB, BNIP2, PPP3CB) that could be regulated by RBPs. The co-expression network was used to further elucidate the regulatory and interaction relationship between RBPs and AS genes. Apoptotic process and innate immune response, revealed by the functional enrichment analysis of RASGs regulated by RBPs were closely related to atherosclerosis. In addition, 26 of the 344 alternative splicing genes regulated by the above 10 RBPs were transcription factors (TFs), We selected high expression nine TFs (TFDP1, RBBP7, STAT2, CREB5, ERG, ELF1, HMGN3, BCLAF1, and ZEB2) for co-expression analysis. The target genes of these TFs were mainly enriched in inflammatory and immune response pathways that were associated with atherosclerosis. indicating that AS abnormalities of these TFs may have a function in atherosclerosis. Furthermore, the expression of differentially expressed RBPs and the alternative splicing events of AS genes was validated by qRT-PCR in umbilical vein endothelial cells (HUVEC). The results showed that RBM47 were remarkedly difference in HUVEC treated with ox-LDL and the splicing ratio of AS in BCLAF1which is regulated by RBM47 significantly changed. In conclusion, the differentially expressed RBPs identified in our analysis may play important roles in the development of atherosclerosis by regulating the AS of these TF genes.
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Affiliation(s)
- Runqing Wang
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, Gansu, China.,Gansu Key Laboratory of Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, Gansu, China.,Gansu Clinical Medical Research Center for Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Jin Xu
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, Gansu, China.,Gansu Key Laboratory of Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, Gansu, China.,Gansu Clinical Medical Research Center for Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Yuning Tang
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, Gansu, China.,Gansu Key Laboratory of Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, Gansu, China.,Gansu Clinical Medical Research Center for Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, Gansu, China.,Department of Cardiology, Lanzhou University Second Hospital, Lanzhou, China
| | - Yongxiang Wang
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, Gansu, China.,Gansu Key Laboratory of Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, Gansu, China.,Gansu Clinical Medical Research Center for Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, Gansu, China.,Heart Center, The First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Jing Zhao
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, Gansu, China.,Gansu Key Laboratory of Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, Gansu, China.,Gansu Clinical Medical Research Center for Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, Gansu, China.,Heart Center, The First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Liqiong Ding
- Gansu Key Laboratory of Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, Gansu, China.,Gansu Clinical Medical Research Center for Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, Gansu, China.,Heart Center, The First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Yu Peng
- Gansu Key Laboratory of Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, Gansu, China.,Gansu Clinical Medical Research Center for Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, Gansu, China.,Heart Center, The First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Zheng Zhang
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, Gansu, China. .,Gansu Key Laboratory of Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, Gansu, China. .,Gansu Clinical Medical Research Center for Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, Gansu, China. .,Heart Center, The First Hospital of Lanzhou University, Lanzhou, Gansu, China.
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21
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Boos F, Oo JA, Warwick T, Günther S, Izquierdo Ponce J, Lopez M, Rafii D, Buchmann G, Pham MD, Msheik ZS, Li T, Seredinski S, Haydar S, Kashefiolasl S, Plate KH, Behr R, Mietsch M, Krishnan J, Pullamsetti SS, Bibli SI, Hinkel R, Baker AH, Boon RA, Schulz MH, Wittig I, Miller FJ, Brandes RP, Leisegang MS. The endothelial-enriched lncRNA LINC00607 mediates angiogenic function. Basic Res Cardiol 2023; 118:5. [PMID: 36700983 PMCID: PMC9879848 DOI: 10.1007/s00395-023-00978-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 01/09/2023] [Accepted: 01/09/2023] [Indexed: 01/27/2023]
Abstract
Long non-coding RNAs (lncRNAs) can act as regulatory RNAs which, by altering the expression of target genes, impact on the cellular phenotype and cardiovascular disease development. Endothelial lncRNAs and their vascular functions are largely undefined. Deep RNA-Seq and FANTOM5 CAGE analysis revealed the lncRNA LINC00607 to be highly enriched in human endothelial cells. LINC00607 was induced in response to hypoxia, arteriosclerosis regression in non-human primates, post-atherosclerotic cultured endothelial cells from patients and also in response to propranolol used to induce regression of human arteriovenous malformations. siRNA knockdown or CRISPR/Cas9 knockout of LINC00607 attenuated VEGF-A-induced angiogenic sprouting. LINC00607 knockout in endothelial cells also integrated less into newly formed vascular networks in an in vivo assay in SCID mice. Overexpression of LINC00607 in CRISPR knockout cells restored normal endothelial function. RNA- and ATAC-Seq after LINC00607 knockout revealed changes in the transcription of endothelial gene sets linked to the endothelial phenotype and in chromatin accessibility around ERG-binding sites. Mechanistically, LINC00607 interacted with the SWI/SNF chromatin remodeling protein BRG1. CRISPR/Cas9-mediated knockout of BRG1 in HUVEC followed by CUT&RUN revealed that BRG1 is required to secure a stable chromatin state, mainly on ERG-binding sites. In conclusion, LINC00607 is an endothelial-enriched lncRNA that maintains ERG target gene transcription by interacting with the chromatin remodeler BRG1 to ultimately mediate angiogenesis.
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Affiliation(s)
- Frederike Boos
- Institut für Kardiovaskuläre Physiologie, Fachbereich Medizin der Goethe-Universität, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
- German Center of Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt, Germany
| | - James A Oo
- Institut für Kardiovaskuläre Physiologie, Fachbereich Medizin der Goethe-Universität, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
- German Center of Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt, Germany
| | - Timothy Warwick
- Institut für Kardiovaskuläre Physiologie, Fachbereich Medizin der Goethe-Universität, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
- German Center of Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt, Germany
| | - Stefan Günther
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Judit Izquierdo Ponce
- Institut für Kardiovaskuläre Physiologie, Fachbereich Medizin der Goethe-Universität, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Melina Lopez
- Institut für Kardiovaskuläre Physiologie, Fachbereich Medizin der Goethe-Universität, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
- German Center of Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt, Germany
| | - Diba Rafii
- Institut für Kardiovaskuläre Physiologie, Fachbereich Medizin der Goethe-Universität, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
- German Center of Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt, Germany
| | - Giulia Buchmann
- Institut für Kardiovaskuläre Physiologie, Fachbereich Medizin der Goethe-Universität, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
- German Center of Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt, Germany
| | - Minh Duc Pham
- Genome Biologics, Frankfurt, Germany
- Institute for Cardiovascular Regeneration, Goethe University, Frankfurt, Germany
| | - Zahraa S Msheik
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
- Department of Internal Medicine, Member of the DZL, Member of Cardio-Pulmonary Institute (CPI), Justus Liebig University, Giessen, Germany
| | - Tianfu Li
- Institut für Kardiovaskuläre Physiologie, Fachbereich Medizin der Goethe-Universität, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
- German Center of Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt, Germany
| | - Sandra Seredinski
- Institut für Kardiovaskuläre Physiologie, Fachbereich Medizin der Goethe-Universität, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
- German Center of Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt, Germany
| | - Shaza Haydar
- Institut für Kardiovaskuläre Physiologie, Fachbereich Medizin der Goethe-Universität, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
- German Center of Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt, Germany
| | - Sepide Kashefiolasl
- Department of Neurosurgery, University Hospital Frankfurt, Frankfurt, Germany
| | - Karl H Plate
- Institute of Neurology (Edinger Institute), Neuroscience Center, Goethe University, Frankfurt, Germany
- Frankfurt Cancer Institute, University Hospital, Goethe University, Frankfurt, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Frankfurt, Germany
- German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Rüdiger Behr
- DZHK (German Center for Cardiovascular Research), Partner Site Göttingen, Göttingen, Germany
- Platform Degenerative Diseases, German Primate Center-Leibniz Institute for Primate Research, Göttingen, Germany
| | - Matthias Mietsch
- DZHK (German Center for Cardiovascular Research), Partner Site Göttingen, Göttingen, Germany
- Laboratory Animal Science Unit, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Jaya Krishnan
- German Center of Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt, Germany
- Institute for Cardiovascular Regeneration, Goethe University, Frankfurt, Germany
- Cardio-Pulmonary Institute, Giessen, Germany
- Department of Medicine III, Cardiology/Angiology/Nephrology, Goethe University Hospital, Frankfurt am Main, Germany
| | - Soni S Pullamsetti
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
- Department of Internal Medicine, Member of the DZL, Member of Cardio-Pulmonary Institute (CPI), Justus Liebig University, Giessen, Germany
- Cardio-Pulmonary Institute, Giessen, Germany
| | - Sofia-Iris Bibli
- German Center of Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt, Germany
- Institute for Vascular Signalling, Goethe University, Frankfurt, Germany
| | - Rabea Hinkel
- DZHK (German Center for Cardiovascular Research), Partner Site Göttingen, Göttingen, Germany
- Laboratory Animal Science Unit, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
- Institute for Animal Hygiene, Animal Welfare and Farm Animal Behavior, University of Veterinary Medicine, Hannover, Germany
| | - Andrew H Baker
- Centre for Cardiovascular Science, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, Scotland
- CARIM Institute, University of Maastricht, Maastricht, The Netherlands
| | - Reinier A Boon
- German Center of Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt, Germany
- Institute for Cardiovascular Regeneration, Goethe University, Frankfurt, Germany
- Department of Physiology, Amsterdam Cardiovascular Sciences, VU Medical Center, Amsterdam UMC, Amsterdam, The Netherlands
| | - Marcel H Schulz
- German Center of Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt, Germany
- Institute for Cardiovascular Regeneration, Goethe University, Frankfurt, Germany
| | - Ilka Wittig
- Institut für Kardiovaskuläre Physiologie, Fachbereich Medizin der Goethe-Universität, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
- German Center of Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt, Germany
| | - Francis J Miller
- Department of Medicine, Vanderbilt University Medical Center, Nashville, USA
- Veterans Affairs Medical Center, Nashville, TN, USA
| | - Ralf P Brandes
- Institut für Kardiovaskuläre Physiologie, Fachbereich Medizin der Goethe-Universität, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany.
- German Center of Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt, Germany.
| | - Matthias S Leisegang
- Institut für Kardiovaskuläre Physiologie, Fachbereich Medizin der Goethe-Universität, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany.
- German Center of Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt, Germany.
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22
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Kodgule R, Goldman JW, Monovich AC, Saari T, Aguilar AR, Hall CN, Rajesh N, Gupta J, Chu SCA, Ye L, Gurumurthy A, Iyer A, Brown NA, Chiang MY, Cieslik MP, Ryan RJ. ETV6 Deficiency Unlocks ERG-Dependent Microsatellite Enhancers to Drive Aberrant Gene Activation in B-Lymphoblastic Leukemia. Blood Cancer Discov 2023; 4:34-53. [PMID: 36350827 PMCID: PMC9820540 DOI: 10.1158/2643-3230.bcd-21-0224] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 08/30/2022] [Accepted: 11/02/2022] [Indexed: 11/11/2022] Open
Abstract
Distal enhancers play critical roles in sustaining oncogenic gene-expression programs. We identify aberrant enhancer-like activation of GGAA tandem repeats as a characteristic feature of B-cell acute lymphoblastic leukemia (B-ALL) with genetic defects of the ETV6 transcriptional repressor, including ETV6-RUNX1+ and ETV6-null B-ALL. We show that GGAA repeat enhancers are direct activators of previously identified ETV6-RUNX1+/- like B-ALL "signature" genes, including the likely leukemogenic driver EPOR. When restored to ETV6-deficient B-ALL cells, ETV6 directly binds to GGAA repeat enhancers, represses their acetylation, downregulates adjacent genes, and inhibits B-ALL growth. In ETV6-deficient B-ALL cells, we find that the ETS transcription factor ERG directly binds to GGAA microsatellite enhancers and is required for sustained activation of repeat enhancer-activated genes. Together, our findings reveal an epigenetic gatekeeper function of the ETV6 tumor suppressor gene and establish microsatellite enhancers as a key mechanism underlying the unique gene-expression program of ETV6-RUNX1+/- like B-ALL. SIGNIFICANCE We find a unifying mechanism underlying a leukemia subtype-defining gene-expression signature that relies on repetitive elements with poor conservation between humans and rodents. The ability of ETV6 to antagonize promiscuous, nonphysiologic ERG activity may shed light on other roles of these key regulators in hematolymphoid development and human disease. See related commentary by Mercher, p. 2. This article is highlighted in the In This Issue feature, p. 1.
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Affiliation(s)
- Rohan Kodgule
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Joshua W. Goldman
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan
| | | | - Travis Saari
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Athalee R. Aguilar
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Cody N. Hall
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Niharika Rajesh
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Juhi Gupta
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Shih-Chun A. Chu
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Li Ye
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Aishwarya Gurumurthy
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Ashwin Iyer
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Noah A. Brown
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Mark Y. Chiang
- Department of Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - Marcin P. Cieslik
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Russell J.H. Ryan
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
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23
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Lian D, Lian L, Zeng D, Zhang M, Chen M, Liu Y, Ying W, Zhou S. Identification of prognostic values of the transcription factor-CpG-gene triplets in lung adenocarcinoma: A narrative review. Medicine (Baltimore) 2022; 101:e32045. [PMID: 36550923 PMCID: PMC9771220 DOI: 10.1097/md.0000000000032045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVE Abnormal DNA methylation can regulate carcinogenesis in lung adenocarcinoma (LUAD), while transcription factors (TFs) mediate methylation in a site-specific manner to affect downstream transcriptional regulation and tumor progression. Therefore, this study aimed to explore the TF-methylation-gene regulatory relationships that influence LUAD prognosis. METHODS Differential analyses of methylation sites and genes were generated by integrating transcriptome and methylome profiles from public databases. Through target gene identification, motif enrichment in the promoter region, and TF prediction, TF-methylation and methylation-gene relation pairs were obtained. Then, the prognostic TF-methylation-gene network was constructed using univariate Cox regression analysis. Prognostic models were constructed based on the key regulatory axes. Finally, Kaplan-Meier curves were created to evaluate the model efficacy and the relationship between candidate genes and prognosis. RESULTS A total of 1878 differential expressed genes and 1233 differential methylation sites were screened between LUAD and normal samples. Then 10 TFs were predicted to bind 144 enriched motifs. After integrating TF-methylation and methylation-gene relations, a prognostic TF-methylation-gene network containing 4 TFs, 111 methylation sites, and 177 genes was constructed. In this network, ERG-cg27071152-MTURN and FOXM1-cg19212949-PTPR regulatory axes were selected to construct the prognostic models, which showed robust abilities in predicting 1-, 3-, and 5-year survival probabilities. Finally, ERG and MTURN were downregulated in LUAD samples, whereas FOXM1 and PTPR were upregulated. Their expression levels were related to LUAD prognosis. CONCLUSION ERG-cg27071152-MTURN and FOXM1-cg19212949-PTPR regulatory axes were proposed as potential biomarkers for predicting the prognosis of LUAD.
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Affiliation(s)
- Duohuang Lian
- Department of Thoracic and Cardiac Surgery, The 900th Hospital of The Joint Logistics Support Force of The People's Liberation Army, Fuzhou City, Fujian Province, China
| | - Luoyu Lian
- Department of Thoracic Surgery, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou City, Fujian Province, China
| | - Dehua Zeng
- Department of Pathology, The 900th Hospital of The Joint Logistics Support Force of The Chinese People's Liberation Army, Fuzhou City, Fujian Province, China
| | - Meiqing Zhang
- Department of Thoracic and Cardiac Surgery, The 900th Hospital of The Joint Logistics Support Force of The People's Liberation Army, Fuzhou City, Fujian Province, China
| | - Mengmeng Chen
- Department of Thoracic and Cardiac Surgery, The 900th Hospital of The Joint Logistics Support Force of The People's Liberation Army, Fuzhou City, Fujian Province, China
| | - Yaming Liu
- Department of Thoracic and Cardiac Surgery, The 900th Hospital of The Joint Logistics Support Force of The People's Liberation Army, Fuzhou City, Fujian Province, China
| | - Wenmin Ying
- Department of Radiotherapy, Fuding Hospital, Fuding City, Fujian Province, China
- * Correspondance: Wenmin Ying, Department of Radiotherapy, Fuding Hospital, Fuding City, Fujian Province 355200, China (e-mail: )
| | - Shunkai Zhou
- Department of Thoracic and Cardiac Surgery, The 900th Hospital of The Joint Logistics Support Force of The People's Liberation Army, Fuzhou City, Fujian Province, China
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24
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Wang Y, Song C, Zhao J, Zhang Y, Zhao X, Feng C, Zhang G, Zhu J, Wang F, Qian F, Zhou L, Zhang J, Bai X, Ai B, Liu X, Wang Q, Li C. SEdb 2.0: a comprehensive super-enhancer database of human and mouse. Nucleic Acids Res 2022; 51:D280-D290. [PMID: 36318264 PMCID: PMC9825585 DOI: 10.1093/nar/gkac968] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/09/2022] [Accepted: 10/13/2022] [Indexed: 01/09/2023] Open
Abstract
Super-enhancers (SEs) are cell-specific DNA cis-regulatory elements that can supervise the transcriptional regulation processes of downstream genes. SEdb 2.0 (http://www.licpathway.net/sedb) aims to provide a comprehensive SE resource and annotate their potential roles in gene transcriptions. Compared with SEdb 1.0, we have made the following improvements: (i) Newly added the mouse SEs and expanded the scale of human SEs. SEdb 2.0 contained 1 167 518 SEs from 1739 human H3K27ac chromatin immunoprecipitation sequencing (ChIP-seq) samples and 550 226 SEs from 931 mouse H3K27ac ChIP-seq samples, which was five times that of SEdb 1.0. (ii) Newly added transcription factor binding sites (TFBSs) in SEs identified by TF motifs and TF ChIP-seq data. (iii) Added comprehensive (epi)genetic annotations of SEs, including chromatin accessibility regions, methylation sites, chromatin interaction regions and topologically associating domains (TADs). (iv) Newly embedded and updated search and analysis tools, including 'Search SE by TF-based', 'Differential-Overlapping-SE analysis' and 'SE-based TF-Gene analysis'. (v) Newly provided quality control (QC) metrics for ChIP-seq processing. In summary, SEdb 2.0 is a comprehensive update of SEdb 1.0, which curates more SEs and annotation information than SEdb 1.0. SEdb 2.0 provides a friendly platform for researchers to more comprehensively clarify the important role of SEs in the biological process.
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Affiliation(s)
| | | | | | | | - Xilong Zhao
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Chenchen Feng
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Guorui Zhang
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China,School of Computer, University of South China, Hengyang, Hunan 421001, China
| | - Jiang Zhu
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Fan Wang
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Fengcui Qian
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China,School of Computer, University of South China, Hengyang, Hunan 421001, China,The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Liwei Zhou
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China,School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Jian Zhang
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Xuefeng Bai
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Bo Ai
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Xinyu Liu
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Qiuyu Wang
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China,School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China,School of Computer, University of South China, Hengyang, Hunan 421001, China,The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China,Hunan Provincial Base for Scientific and Technological Innovation Cooperation, University of South China, Hengyang, Hunan 421001, China,The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China,Hengyang, Hunan 421001, China,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China,Department of Cell Biology and Genetics, School of Basic Medical Sciences, Hengyang Medical School, University of South China,Hengyang, Hunan 421001, China
| | - Chunquan Li
- To whom correspondence should be addressed. Tel: +86 13272311691; Fax: +86 0734 8279018;
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25
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Wang C, Xing Y, Zhang J, He M, Dong J, Chen S, Wu H, Huang HY, Chou CH, Bai L, He F, She J, Su A, Wang Y, Thistlethwaite PA, Huang HD, Yuan JXJ, Yuan ZY, Shyy JYJ. MED1 Regulates BMP/TGF-β in Endothelium: Implication for Pulmonary Hypertension. Circ Res 2022; 131:828-841. [PMID: 36252121 DOI: 10.1161/circresaha.122.321532] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
BACKGROUND Dysregulated BMP (bone morphogenetic protein) or TGF-β (transforming growth factor beta) signaling pathways are imperative in idiopathic and familial pulmonary arterial hypertension (PAH) as well as experimental pulmonary hypertension (PH) in rodent models. MED1 (mediator complex subunit 1) is a key transcriptional co-activator and KLF4 (Krüppel-like factor 4) is a master transcription factor in endothelium. However, MED1 and KLF4 epigenetic and transcriptional regulations of the BMP/TGF-β axes in pulmonary endothelium and their dysregulations leading to PAH remain elusive. We investigate the MED1/KLF4 co-regulation of the BMP/TGF-β axes in endothelium by studying the epigenetic regulation of BMPR2 (BMP receptor type II), ETS-related gene (ERG), and TGFBR2 (TGF-β receptor 2) and their involvement in the PH. METHODS High-throughput screening involving data from RNA-seq, MED1 ChIP-seq, H3K27ac ChIP-seq, ATAC-seq, and high-throughput chromosome conformation capture together with in silico computations were used to explore the epigenetic and transcriptional regulation of BMPR2, ERG, and TGFBR2 by MED1 and KLF4. In vitro experiments with cultured pulmonary arterial endothelial cells (ECs) and bulk assays were used to validate results from these in silico analyses. Lung tissue from patients with idiopathic PAH, animals with experimental PH, and mice with endothelial ablation of MED1 (EC-MED1-/-) were used to study the PH-protective effect of MED1. RESULTS Levels of MED1 were decreased in lung tissue or pulmonary arterial endothelial cells from idiopathic PAH patients and rodent PH models. Mechanistically, MED1 acted synergistically with KLF4 to transactivate BMPR2, ERG, and TGFBR2 via chromatin remodeling and enhancer-promoter interactions. EC-MED1-/- mice showed PH susceptibility. In contrast, MED1 overexpression mitigated the PH phenotype in rodents. CONCLUSIONS A homeostatic regulation of BMPR2, ERG, and TGFBR2 in ECs by MED1 synergistic with KLF4 is essential for the normal function of the pulmonary endothelium. Dysregulation of MED1 and the resulting impairment of the BMP/TGF-β signaling is implicated in the disease progression of PAH in humans and PH in rodent models.
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Affiliation(s)
- Chen Wang
- Department of Cardiology, First Affiliated Hospital of Xi'an Jiaotong University, China (C.W., Y.X., J.Z., J.D., H.W., L.B., J.S., Z.-Y.).,Cardiovascular Research Center, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, China (C.W., Y.X., J.Z., J.D., S.C., L.B., F.H., A.S.)
| | - Yuanming Xing
- Department of Cardiology, First Affiliated Hospital of Xi'an Jiaotong University, China (C.W., Y.X., J.Z., J.D., H.W., L.B., J.S., Z.-Y.).,Cardiovascular Research Center, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, China (C.W., Y.X., J.Z., J.D., S.C., L.B., F.H., A.S.)
| | - Jiao Zhang
- Department of Cardiology, First Affiliated Hospital of Xi'an Jiaotong University, China (C.W., Y.X., J.Z., J.D., H.W., L.B., J.S., Z.-Y.).,Cardiovascular Research Center, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, China (C.W., Y.X., J.Z., J.D., S.C., L.B., F.H., A.S.).,Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA (J.Z., M.H., J.D., J.Y.-J.)
| | - Ming He
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA (J.Z., M.H., J.D., J.Y.-J.)
| | - Jianjie Dong
- Department of Cardiology, First Affiliated Hospital of Xi'an Jiaotong University, China (C.W., Y.X., J.Z., J.D., H.W., L.B., J.S., Z.-Y.).,Cardiovascular Research Center, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, China (C.W., Y.X., J.Z., J.D., S.C., L.B., F.H., A.S.).,Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA (J.Z., M.H., J.D., J.Y.-J.)
| | - Shanshan Chen
- Cardiovascular Research Center, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, China (C.W., Y.X., J.Z., J.D., S.C., L.B., F.H., A.S.)
| | - Haoyu Wu
- Department of Cardiology, First Affiliated Hospital of Xi'an Jiaotong University, China (C.W., Y.X., J.Z., J.D., H.W., L.B., J.S., Z.-Y.)
| | - Hsi-Yuan Huang
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong-Shenzhen, Shenzhen, China (H.-Y.H., H.-D.H.).,School of Life and Health Sciences, The Chinese University of Hong Kong-Shenzhen, Shenzhen, China (H.-Y.H., H.-D.H.)
| | - Chih-Hung Chou
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan (C.-H.C.)
| | - Liang Bai
- Department of Cardiology, First Affiliated Hospital of Xi'an Jiaotong University, China (C.W., Y.X., J.Z., J.D., H.W., L.B., J.S., Z.-Y.)
| | - Fangzhou He
- Cardiovascular Research Center, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, China (C.W., Y.X., J.Z., J.D., S.C., L.B., F.H., A.S.)
| | - Jianqing She
- Department of Cardiology, First Affiliated Hospital of Xi'an Jiaotong University, China (C.W., Y.X., J.Z., J.D., H.W., L.B., J.S., Z.-Y.)
| | - Ailing Su
- Cardiovascular Research Center, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, China (C.W., Y.X., J.Z., J.D., S.C., L.B., F.H., A.S.)
| | - Youhua Wang
- Institute of Sports and Exercise Biology, School of Physical Education, Shaanxi Normal University, Xi'an, China (Y.W.)
| | - Patricia A Thistlethwaite
- Division of Cardiothoracic Surgery, Department of Surgery, University of California, San Diego, La Jolla, CA (P.A.T.)
| | - Hsien-Da Huang
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong-Shenzhen, Shenzhen, China (H.-Y.H., H.-D.H.).,School of Life and Health Sciences, The Chinese University of Hong Kong-Shenzhen, Shenzhen, China (H.-Y.H., H.-D.H.)
| | - Jason X-J Yuan
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA (J.X.-J.Y.)
| | - Zu-Yi Yuan
- Department of Cardiology, First Affiliated Hospital of Xi'an Jiaotong University, China (C.W., Y.X., J.Z., J.D., H.W., L.B., J.S., Z.-Y.)
| | - John Y-J Shyy
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA (J.Z., M.H., J.D., J.Y.-J.)
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26
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Gomez-Salinero JM, Itkin T, Houghton S, Badwe C, Lin Y, Kalna V, Dufton N, Peghaire CR, Yokoyama M, Wingo M, Lu TM, Li G, Xiang JZ, Hsu YMS, Redmond D, Schreiner R, Birdsey GM, Randi AM, Rafii S. Cooperative ETS Transcription Factors Enforce Adult Endothelial Cell Fate and Cardiovascular Homeostasis. NATURE CARDIOVASCULAR RESEARCH 2022; 1:882-899. [PMID: 36713285 PMCID: PMC7614113 DOI: 10.1038/s44161-022-00128-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 08/04/2022] [Indexed: 01/31/2023]
Abstract
Current dogma dictates that during adulthood, endothelial cells (ECs) are locked in an immutable stable homeostatic state. By contrast, herein we show that maintenance of EC fate and function are linked and active processes, which depend on the constitutive cooperativity of only two ETS-transcription factors (TFs) ERG and Fli1. While deletion of either Fli1 or ERG manifest subtle vascular dysfunction, their combined genetic deletion in adult EC results in acute vasculopathy and multiorgan failure, due to loss of EC fate and integrity, hyperinflammation, and spontaneous thrombosis, leading to death. ERG and Fli1 co-deficiency cause rapid transcriptional silencing of pan- and organotypic vascular core genes, with dysregulation of inflammation and coagulation pathways. Vascular hyperinflammation leads to impaired hematopoiesis with myeloid skewing. Accordingly, enforced ERG and FLI1 expression in adult human mesenchymal stromal cells activates vascular programs and functionality enabling engraftment of perfusable vascular network. GWAS-analysis identified vascular diseases are associated with FLI1/Erg mutations. Constitutive expression of ERG and Fli1 uphold EC fate, physiological function, and resilience in adult vasculature; while their functional loss can contribute to systemic human diseases.
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Affiliation(s)
- Jesus M Gomez-Salinero
- Division of Regenerative Medicine, Hartman Institute for Therapeutic Organ Regeneration, Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, NY, USA
| | - Tomer Itkin
- Division of Regenerative Medicine, Hartman Institute for Therapeutic Organ Regeneration, Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, NY, USA
| | - Sean Houghton
- Division of Regenerative Medicine, Hartman Institute for Therapeutic Organ Regeneration, Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, NY, USA
| | - Chaitanya Badwe
- Division of Regenerative Medicine, Hartman Institute for Therapeutic Organ Regeneration, Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, NY, USA
| | - Yang Lin
- Division of Regenerative Medicine, Hartman Institute for Therapeutic Organ Regeneration, Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, NY, USA
| | - Viktoria Kalna
- National Heart and Lung Institute, Imperial College London, London, UK
- Human Genetics and Computational Biology GSK, UK (current address)
| | - Neil Dufton
- National Heart and Lung Institute, Imperial College London, London, UK
- Queen Mary University of London, Centre for Microvascular Research, William Harvey Research Centre, UK (current address)
| | - Claire R Peghaire
- National Heart and Lung Institute, Imperial College London, London, UK
- University of Bordeaux, Inserm UMR1034, Biology of Cardiovascular Diseases, Pessac, France (current address)
| | - Masataka Yokoyama
- Division of Regenerative Medicine, Hartman Institute for Therapeutic Organ Regeneration, Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, NY, USA
| | - Matthew Wingo
- Division of Regenerative Medicine, Hartman Institute for Therapeutic Organ Regeneration, Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, NY, USA
| | - Tyler M. Lu
- Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Ge Li
- Division of Regenerative Medicine, Hartman Institute for Therapeutic Organ Regeneration, Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, NY, USA
| | | | - Yen-Michael Sheng Hsu
- Division of Regenerative Medicine, Hartman Institute for Therapeutic Organ Regeneration, Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, NY, USA
- Division of Hematology/Oncology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA (current address)
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA (current address)
| | - David Redmond
- Division of Regenerative Medicine, Hartman Institute for Therapeutic Organ Regeneration, Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, NY, USA
| | - Ryan Schreiner
- Division of Regenerative Medicine, Hartman Institute for Therapeutic Organ Regeneration, Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, NY, USA
| | - Graeme M Birdsey
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Anna M Randi
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Shahin Rafii
- Division of Regenerative Medicine, Hartman Institute for Therapeutic Organ Regeneration, Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, NY, USA
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27
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Stefanucci L, Frontini M. Non-coding genetic variation in regulatory elements determines thrombosis and hemostasis phenotypes. J Thromb Haemost 2022; 20:1759-1765. [PMID: 35514262 PMCID: PMC9540108 DOI: 10.1111/jth.15754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/27/2022] [Accepted: 05/02/2022] [Indexed: 11/26/2022]
Abstract
Since the early inception of genome-wide association studies (GWAS), it became clear that, in all diseases or traits studied, most genetic variants are likely to exert their effect on gene expression mainly by altering the function of regulatory elements. At the same time, the regulation of the gene expression field broadened its boundaries, from the univocal relationship between regulatory elements and genes to include genome organization, long-range DNA interactions, and epigenetics. Next-generation sequencing has introduced genome-wide approaches that have greatly improved our understanding of the general principles of gene expression. However, elucidating how these apply in every single genomic locus still requires painstaking experimental work, in which several independent lines of evidence are required, and often this is helped by rare genetic variants in individuals with rare diseases. This review will focus on the non-coding features of the genome involved in transcriptional regulation, that when altered, leads to known cases of inherited (familial) thrombotic and hemostatic phenotypes, emphasizing the role of enhancers and super-enhancers.
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Affiliation(s)
- Luca Stefanucci
- Department of HaematologyUniversity of Cambridge, Cambridge Biomedical CampusCambridgeUK
- National Health Service (NHS) Blood and TransplantCambridge Biomedical CampusCambridgeUK
- British Heart Foundation, Cambridge Centre for Research ExcellenceUniversity of Cambridge, Cambridge Biomedical CampusCambridgeUK
| | - Mattia Frontini
- Department of HaematologyUniversity of Cambridge, Cambridge Biomedical CampusCambridgeUK
- National Health Service (NHS) Blood and TransplantCambridge Biomedical CampusCambridgeUK
- British Heart Foundation, Cambridge Centre for Research ExcellenceUniversity of Cambridge, Cambridge Biomedical CampusCambridgeUK
- Institute of Biomedical & Clinical Science, College of Medicine and HealthUniversity of Exeter Medical SchoolExeterUK
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28
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Fuglerud BM, Drissler S, Lotto J, Stephan TL, Thakur A, Cullum R, Hoodless PA. SOX9 reprograms endothelial cells by altering the chromatin landscape. Nucleic Acids Res 2022; 50:8547-8565. [PMID: 35904801 PMCID: PMC9410909 DOI: 10.1093/nar/gkac652] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 06/15/2022] [Accepted: 07/20/2022] [Indexed: 01/08/2023] Open
Abstract
The transcription factor SOX9 is activated at the onset of endothelial-to-mesenchymal transition (EndMT) during embryonic development and in pathological conditions. Its roles in regulating these processes, however, are not clear. Using human umbilical vein endothelial cells (HUVECs) as an EndMT model, we show that SOX9 expression alone is sufficient to activate mesenchymal genes and steer endothelial cells towards a mesenchymal fate. By genome-wide mapping of the chromatin landscape, we show that SOX9 displays features of a pioneer transcription factor, such as opening of chromatin and leading to deposition of active histone modifications at silent chromatin regions, guided by SOX dimer motifs and H2A.Z enrichment. We further observe highly transient and dynamic SOX9 binding, possibly promoted through its eviction by histone phosphorylation. However, while SOX9 binding is dynamic, changes in the chromatin landscape and cell fate induced by SOX9 are persistent. Finally, our analysis of single-cell chromatin accessibility indicates that SOX9 opens chromatin to drive EndMT in atherosclerotic lesions in vivo. This study provides new insight into key molecular functions of SOX9 and mechanisms of EndMT and highlights the crucial developmental role of SOX9 and relevance to human disease.
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Affiliation(s)
- Bettina M Fuglerud
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada.,Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Sibyl Drissler
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada.,Cell and Developmental Biology Program, University of British Columbia V6T 1Z3, Vancouver, British Columbia, Canada
| | - Jeremy Lotto
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada.,Cell and Developmental Biology Program, University of British Columbia V6T 1Z3, Vancouver, British Columbia, Canada
| | - Tabea L Stephan
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada.,Cell and Developmental Biology Program, University of British Columbia V6T 1Z3, Vancouver, British Columbia, Canada
| | - Avinash Thakur
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada
| | - Rebecca Cullum
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada
| | - Pamela A Hoodless
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada.,Cell and Developmental Biology Program, University of British Columbia V6T 1Z3, Vancouver, British Columbia, Canada.,School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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29
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Caporarello N, Lee J, Pham TX, Jones DL, Guan J, Link PA, Meridew JA, Marden G, Yamashita T, Osborne CA, Bhagwate AV, Huang SK, Nicosia RF, Tschumperlin DJ, Trojanowska M, Ligresti G. Dysfunctional ERG signaling drives pulmonary vascular aging and persistent fibrosis. Nat Commun 2022; 13:4170. [PMID: 35879310 PMCID: PMC9314350 DOI: 10.1038/s41467-022-31890-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 07/04/2022] [Indexed: 01/18/2023] Open
Abstract
Vascular dysfunction is a hallmark of chronic diseases in elderly. The contribution of the vasculature to lung repair and fibrosis is not fully understood. Here, we performed an epigenetic and transcriptional analysis of lung endothelial cells (ECs) from young and aged mice during the resolution or progression of bleomycin-induced lung fibrosis. We identified the transcription factor ETS-related gene (ERG) as putative orchestrator of lung capillary homeostasis and repair, and whose function is dysregulated in aging. ERG dysregulation is associated with reduced chromatin accessibility and maladaptive transcriptional responses to injury. Loss of endothelial ERG enhances paracrine fibroblast activation in vitro, and impairs lung fibrosis resolution in young mice in vivo. scRNA-seq of ERG deficient mouse lungs reveales transcriptional and fibrogenic abnormalities resembling those associated with aging and human lung fibrosis, including reduced number of general capillary (gCap) ECs. Our findings demonstrate that lung endothelial chromatin remodeling deteriorates with aging leading to abnormal transcription, vascular dysrepair, and persistent fibrosis following injury.
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Affiliation(s)
- Nunzia Caporarello
- Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - Jisu Lee
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Tho X Pham
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Dakota L Jones
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jiazhen Guan
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Patrick A Link
- Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - Jeffrey A Meridew
- Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - Grace Marden
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Takashi Yamashita
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Collin A Osborne
- Department of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Aditya V Bhagwate
- Department of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Steven K Huang
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Roberto F Nicosia
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | | | - Maria Trojanowska
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Giovanni Ligresti
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA.
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30
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Panara V, Monteiro R, Koltowska K. Epigenetic Regulation of Endothelial Cell Lineages During Zebrafish Development-New Insights From Technical Advances. Front Cell Dev Biol 2022; 10:891538. [PMID: 35615697 PMCID: PMC9125237 DOI: 10.3389/fcell.2022.891538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 04/10/2022] [Indexed: 01/09/2023] Open
Abstract
Epigenetic regulation is integral in orchestrating the spatiotemporal regulation of gene expression which underlies tissue development. The emergence of new tools to assess genome-wide epigenetic modifications has enabled significant advances in the field of vascular biology in zebrafish. Zebrafish represents a powerful model to investigate the activity of cis-regulatory elements in vivo by combining technologies such as ATAC-seq, ChIP-seq and CUT&Tag with the generation of transgenic lines and live imaging to validate the activity of these regulatory elements. Recently, this approach led to the identification and characterization of key enhancers of important vascular genes, such as gata2a, notch1b and dll4. In this review we will discuss how the latest technologies in epigenetics are being used in the zebrafish to determine chromatin states and assess the function of the cis-regulatory sequences that shape the zebrafish vascular network.
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Affiliation(s)
- Virginia Panara
- Immunology Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Rui Monteiro
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom,Birmingham Centre of Genome Biology, University of Birmingham, Birmingham, United Kingdom
| | - Katarzyna Koltowska
- Immunology Genetics and Pathology, Uppsala University, Uppsala, Sweden,*Correspondence: Katarzyna Koltowska,
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31
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He Y, Tacconi C, Dieterich LC, Kim J, Restivo G, Gousopoulos E, Lindenblatt N, Levesque MP, Claassen M, Detmar M. Novel Blood Vascular Endothelial Subtype-Specific Markers in Human Skin Unearthed by Single-Cell Transcriptomic Profiling. Cells 2022; 11:cells11071111. [PMID: 35406678 PMCID: PMC8997372 DOI: 10.3390/cells11071111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 02/04/2023] Open
Abstract
Ample evidence pinpoints the phenotypic diversity of blood vessels (BVs) and site-specific functions of their lining endothelial cells (ECs). We harnessed single-cell RNA sequencing (scRNA-seq) to dissect the molecular heterogeneity of blood vascular endothelial cells (BECs) in healthy adult human skin and identified six different subpopulations, signifying arterioles, post-arterial capillaries, pre-venular capillaries, post-capillary venules, venules and collecting venules. Individual BEC subtypes exhibited distinctive transcriptomic landscapes associated with diverse biological pathways. These functionally distinct dermal BV segments were characterized by their unique compositions of conventional and novel markers (e.g., arteriole marker GJA5; arteriole capillary markers ASS1 and S100A4; pre-venular capillary markers SOX17 and PLAUR; venular markers EGR2 and LRG1), many of which have been implicated in vascular remodeling upon inflammatory responses. Immunofluorescence staining of human skin sections and whole-mount skin blocks confirmed the discrete expression of these markers along the blood vascular tree in situ, further corroborating BEC heterogeneity in human skin. Overall, our study molecularly refines individual BV compartments, whilst the identification of novel subtype-specific signatures provides more insights for future studies dissecting the responses of distinct vessel segments under pathological conditions.
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Affiliation(s)
- Yuliang He
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) Zürich, 8093 Zürich, Switzerland; (Y.H.); (C.T.); (L.C.D.); (J.K.)
| | - Carlotta Tacconi
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) Zürich, 8093 Zürich, Switzerland; (Y.H.); (C.T.); (L.C.D.); (J.K.)
- Department of Biosciences, University of Milan, 20133 Milan, Italy
| | - Lothar C. Dieterich
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) Zürich, 8093 Zürich, Switzerland; (Y.H.); (C.T.); (L.C.D.); (J.K.)
| | - Jihye Kim
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) Zürich, 8093 Zürich, Switzerland; (Y.H.); (C.T.); (L.C.D.); (J.K.)
| | - Gaetana Restivo
- Department of Dermatology, University Hospital Zürich, 8091 Zürich, Switzerland; (G.R.); (M.P.L.)
| | - Epameinondas Gousopoulos
- Department of Plastic Surgery and Hand Surgery, University Hospital Zürich, 8091 Zürich, Switzerland; (E.G.); (N.L.)
| | - Nicole Lindenblatt
- Department of Plastic Surgery and Hand Surgery, University Hospital Zürich, 8091 Zürich, Switzerland; (E.G.); (N.L.)
| | - Mitchell P. Levesque
- Department of Dermatology, University Hospital Zürich, 8091 Zürich, Switzerland; (G.R.); (M.P.L.)
| | - Manfred Claassen
- Department of Internal Medicine I, University of Tübingen, 72074 Tübingen, Germany;
- Department of Computer Science, University of Tübingen, 72074 Tübingen, Germany
| | - Michael Detmar
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) Zürich, 8093 Zürich, Switzerland; (Y.H.); (C.T.); (L.C.D.); (J.K.)
- Correspondence:
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32
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HDAC11 promotes both NLRP3/caspase-1/GSDMD and caspase-3/GSDME pathways causing pyroptosis via ERG in vascular endothelial cells. Cell Death Dis 2022; 8:112. [PMID: 35279683 PMCID: PMC8918356 DOI: 10.1038/s41420-022-00906-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/30/2022] [Accepted: 02/14/2022] [Indexed: 01/03/2023]
Abstract
Histone deacetylase 11 (HDAC11), a sole member of the class IV HDAC subfamily, participates in various cardiovascular diseases. Recent evidence showed that pyroptosis was a form of inflammatory programmed cell death and is critical for atherosclerosis (AS). However, little is known about the effect of HDAC11 on endothelial cell pyroptosis in AS. Thus, this study aims to investigate the role of HDAC11 in vascular endothelial cell pyroptosis and its molecular mechanism. Firstly, we found that HDAC11 expression was up-regulated and pyroptosis occurred in the aorta of ApoE−/− mice fed with a high-fat diet (HFD) for 8 or 12 weeks. Then, in vitro study found the treatment of human umbilical vein endothelial cells (HUVECs) with tumor necrosis factor-α (TNF-α) resulted in pyroptosis, as evidenced by activation of caspase-1 and caspase-3 activation, cleavage of downstream gasdermin D (GSDMD) and gasdermin E (GSDME/DFNA5), the release of pro-inflammatory cytokines interleukin (IL)-1β, IL-6 and IL-18, as well as elevation of LDH activity and increase of propidium iodide (PI)-positive cells. Besides, TNF-α increased HDAC11 expression and induced pyroptosis via TNFR1 in HUVECs. HDAC11 knockdown mitigated pyroptosis by suppressing both NLRP3/caspase-1/GSDMD and caspase-3/GSDME pathways in TNF-α-induced HUVECs. Moreover, GSDME knockdown by siRNA significantly decreased pyroptosis and inflammatory response, while treatment with disulfiram or necrosulfonamide (NSA) further augmented the inhibitory effects of GSDME siRNA on pyroptosis and inflammatory response. Further studies found HDAC11 formed a complex with ERG and decreased the acetylation levels of ERG. More importantly, ERG knockdown augmented vascular endothelial cell pyroptosis in TNF-α-induced HUVECs. Taken together, our study suggests that HDAC11 might promote both NLRP3/caspase-1/GSDMD and caspase-3/GSDME pathways leading to pyroptosis via regulation of ERG acetylation in HUVECs. Modulation of HDAC11 may serve as a potential target for therapeutic strategies of AS.
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33
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Trott AJ, Greenwell BJ, Karhadkar TR, Guerrero-Vargas NN, Escobar C, Buijs RM, Menet JS. Lack of food intake during shift work alters the heart transcriptome and leads to cardiac tissue fibrosis and inflammation in rats. BMC Biol 2022; 20:58. [PMID: 35236346 PMCID: PMC8892784 DOI: 10.1186/s12915-022-01256-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 02/16/2022] [Indexed: 12/14/2022] Open
Abstract
Background Many epidemiological studies revealed that shift work is associated with an increased risk of a number of pathologies, including cardiovascular diseases. An experimental model of shift work in rats has additionally been shown to recapitulate aspects of metabolic disorders observed in human shift workers, including increased fat content and impaired glucose tolerance, and used to demonstrate that restricting food consumption outside working hours prevents shift work-associated obesity and metabolic disturbance. However, the way distinct shift work parameters, such as type of work, quantity, and duration, affect cardiovascular function and the underlying mechanisms, remains poorly understood. Here, we used the rat as a model to characterize the effects of shift work in the heart and determine whether they can be modulated by restricting food intake during the normal active phase. Results We show that experimental shift work reprograms the heart cycling transcriptome independently of food consumption. While phases of rhythmic gene expression are distributed across the 24-h day in control rats, they are clustered towards discrete times in shift workers. Additionally, preventing food intake during shift work affects the expression level of hundreds of genes in the heart, including genes encoding components of the extracellular matrix and inflammatory markers found in transcriptional signatures associated with pressure overload and cardiac hypertrophy. Consistent with this, the heart of shift worker rats not eating during work hours, but having access to food outside of shift work, exhibits increased collagen 1 deposition and displays increased infiltration by immune cells. While maintaining food access during shift work has less effects on gene expression, genes found in transcriptional signatures of cardiac hypertrophy remain affected, and the heart of shift worker rats exhibits fibrosis without inflammation. Conclusions Together, our findings unraveled differential effects of food consumption on remodeled transcriptional profiles of the heart in shift worker rats. They also provide insights into how shift work affects cardiac function and suggest that some interventions aiming at mitigating metabolic disorders in shift workers may have adverse effects on cardiovascular diseases. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01256-9.
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Affiliation(s)
- Alexandra J Trott
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA.,Program of Genetics, Texas A&M University, College Station, TX, 77843, USA.,Center for Biological Clock Research, Texas A&M University, College Station, TX, 77843, USA
| | - Ben J Greenwell
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA.,Program of Genetics, Texas A&M University, College Station, TX, 77843, USA.,Center for Biological Clock Research, Texas A&M University, College Station, TX, 77843, USA
| | - Tejas R Karhadkar
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA.,Program of Genetics, Texas A&M University, College Station, TX, 77843, USA
| | - Natali N Guerrero-Vargas
- Departamento de Anatomía, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico City, Mexico
| | - Carolina Escobar
- Departamento de Anatomía, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico City, Mexico
| | - Ruud M Buijs
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico City, Mexico
| | - Jerome S Menet
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA. .,Program of Genetics, Texas A&M University, College Station, TX, 77843, USA. .,Center for Biological Clock Research, Texas A&M University, College Station, TX, 77843, USA.
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34
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Finding and Verifying Enhancers for Endothelial-Expressed Genes. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2441:351-368. [PMID: 35099751 DOI: 10.1007/978-1-0716-2059-5_28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Identification and analysis of enhancers for endothelial-expressed genes can provide crucial information regarding their upstream transcriptional regulators. However, enhancer identification can be challenging, particularly for people with limited access or experience of bioinformatics, and transgenic analysis of enhancer activity patterns can be prohibitively expensive. Here we describe how to use publicly available datasets displayed on the UCSC Genome Browser to identify putative endothelial enhancers for mammalian genes. Furthermore, we detail how to utilize mosaic Tol2-mediated transgenesis in zebrafish to verify whether a putative enhancer is capable of directing endothelial-specific patterns of gene expression.
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35
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Qian C, Li D, Chen Y. ETS factors in prostate cancer. Cancer Lett 2022; 530:181-189. [PMID: 35033589 PMCID: PMC8832285 DOI: 10.1016/j.canlet.2022.01.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 01/01/2022] [Accepted: 01/10/2022] [Indexed: 12/21/2022]
Abstract
The ETS family of proteins consists of 28 transcription factors, many of which play critical roles in both normal tissue development and homeostasis and have been implicated in development and progression of a variety of cancers. In prostate cancer, gene fusion and overexpression of ETS factors ERG, FLI1, ETV1, ETV4 and ETV5 have been found in half of prostate cancer patients in Caucasian men and define the largest genetic subtype of prostate cancer. This review summarizes the data on the discovery, modeling, molecular taxonomy, lineage plasticity and therapeutic targeting of ETS family members in prostate cancer.
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Affiliation(s)
- Cheng Qian
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA; Department of Urology, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China
| | - Dan Li
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Yu Chen
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, NY, 10065, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, 10065, USA.
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36
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Sun X, Perl AK, Li R, Bell SM, Sajti E, Kalinichenko VV, Kalin TV, Misra RS, Deshmukh H, Clair G, Kyle J, Crotty Alexander LE, Masso-Silva JA, Kitzmiller JA, Wikenheiser-Brokamp KA, Deutsch G, Guo M, Du Y, Morley MP, Valdez MJ, Yu HV, Jin K, Bardes EE, Zepp JA, Neithamer T, Basil MC, Zacharias WJ, Verheyden J, Young R, Bandyopadhyay G, Lin S, Ansong C, Adkins J, Salomonis N, Aronow BJ, Xu Y, Pryhuber G, Whitsett J, Morrisey EE. A census of the lung: CellCards from LungMAP. Dev Cell 2022; 57:112-145.e2. [PMID: 34936882 PMCID: PMC9202574 DOI: 10.1016/j.devcel.2021.11.007] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 07/19/2021] [Accepted: 11/05/2021] [Indexed: 01/07/2023]
Abstract
The human lung plays vital roles in respiration, host defense, and basic physiology. Recent technological advancements such as single-cell RNA sequencing and genetic lineage tracing have revealed novel cell types and enriched functional properties of existing cell types in lung. The time has come to take a new census. Initiated by members of the NHLBI-funded LungMAP Consortium and aided by experts in the lung biology community, we synthesized current data into a comprehensive and practical cellular census of the lung. Identities of cell types in the normal lung are captured in individual cell cards with delineation of function, markers, developmental lineages, heterogeneity, regenerative potential, disease links, and key experimental tools. This publication will serve as the starting point of a live, up-to-date guide for lung research at https://www.lungmap.net/cell-cards/. We hope that Lung CellCards will promote the community-wide effort to establish, maintain, and restore respiratory health.
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Affiliation(s)
- Xin Sun
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Department of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
| | - Anne-Karina Perl
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH 45267, USA
| | - Rongbo Li
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Sheila M Bell
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Eniko Sajti
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Vladimir V Kalinichenko
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH 45267, USA; Center for Lung Regenerative Medicine, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Tanya V Kalin
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH 45267, USA
| | - Ravi S Misra
- Department of Pediatrics Division of Neonatology, The University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Hitesh Deshmukh
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH 45267, USA
| | - Geremy Clair
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jennifer Kyle
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Laura E Crotty Alexander
- Deparment of Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jorge A Masso-Silva
- Deparment of Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Joseph A Kitzmiller
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Kathryn A Wikenheiser-Brokamp
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Division of Pathology and Laboratory Medicine, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Department of Pathology & Laboratory Medicine, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH 45267, USA
| | - Gail Deutsch
- Department of Pathology, University of Washington School of Medicine, Seattle, WA, USA; Department of Laboratories, Seattle Children's Hospital, OC.8.720, 4800 Sand Point Way Northeast, Seattle, WA 98105, USA
| | - Minzhe Guo
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH 45267, USA
| | - Yina Du
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Michael P Morley
- Penn-CHOP Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael J Valdez
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Haoze V Yu
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Kang Jin
- Departments of Biomedical Informatics, Developmental Biology, and Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Eric E Bardes
- Departments of Biomedical Informatics, Developmental Biology, and Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Jarod A Zepp
- Penn-CHOP Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Terren Neithamer
- Penn-CHOP Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Maria C Basil
- Penn-CHOP Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - William J Zacharias
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Department of Internal Medicine, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH 45267, USA
| | - Jamie Verheyden
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Randee Young
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Gautam Bandyopadhyay
- Department of Pediatrics Division of Neonatology, The University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Sara Lin
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Charles Ansong
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Joshua Adkins
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Nathan Salomonis
- Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH 45267, USA; Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Bruce J Aronow
- Departments of Biomedical Informatics, Developmental Biology, and Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Yan Xu
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH 45267, USA
| | - Gloria Pryhuber
- Department of Pediatrics Division of Neonatology, The University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Jeff Whitsett
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH 45267, USA
| | - Edward E Morrisey
- Penn-CHOP Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Mueller R, Chopra A, Dommisch H, Schaefer AS. Periodontitis Risk Variants at SIGLEC5 Impair ERG and MAFB Binding. J Dent Res 2021; 101:551-558. [PMID: 34852650 PMCID: PMC9024020 DOI: 10.1177/00220345211049984] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Periodontitis is a common complex inflammatory disease of the oral cavity. It is characterized by inflammation of gingival tissues and alveolar bone loss. Recently, a genome-wide association study and 2 genome-wide association study meta-analyses found 2 associated regions (haplotype blocks) at the inhibitory immune receptor gene SIGLEC5 to increase the risk for periodontitis. The aims of the current study were the identification of the putative causal variants underlying these associations, characterization of their molecular biological effects, and validation of SIGLEC5 as the target gene. We mapped the associated single-nucleotide polymorphisms to DNA elements with predictive features of regulatory functions and screened the associated alleles for transcription factor (TF) binding sites. Antibody electrophoretic mobility shift assays (EMSAs) with allele-specific probes were used to identify TF binding and to quantify allele-specific effects on binding affinities. Luciferase reporter assays were used to quantify the effect directions and allele-specific strength of the associated regulatory elements. We used CRISPR-dCas9 gene activation to validate SIGLEC5 as a target of the association. EMSA in peripheral blood mononuclear cells showed that E-26 transformation-specific TF-related gene (ERG) binds at rs11084095, with almost complete loss of binding at the minor A-allele. Allele-specific reporter genes showed enhancer function of the DNA sequence at rs11084095, which was abrogated in the background of the A-allele. EMSA in B lymphocytes showed that TF MAF bZIP (MAFB) binds at the common G-allele of rs4284742, whereas the minor A-allele reduced TF binding by 69%, corresponding to 9-fold reduction of luciferase reporter gene activity by the A-allele. Using CRISPR-dCas9, we showed that the enhancer at rs4284742 strongly activated SIGLEC5 expression, validating this gene as the target gene of the association. We conclude that rs11084095 and rs4284742 are putatively causal for the genome-wide significant associations with periodontitis at SIGLEC5 that impair ERG and MAFB binding, respectively.
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Affiliation(s)
- R Mueller
- Department of Periodontology, Oral Medicine and Oral Surgery, Institute for Dental and Craniofacial Sciences, Charité-University Medicine Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Department of Biology, Chemistry and Pharmacy, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - A Chopra
- Department of Periodontology, Oral Medicine and Oral Surgery, Institute for Dental and Craniofacial Sciences, Charité-University Medicine Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - H Dommisch
- Department of Periodontology, Oral Medicine and Oral Surgery, Institute for Dental and Craniofacial Sciences, Charité-University Medicine Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - A S Schaefer
- Department of Periodontology, Oral Medicine and Oral Surgery, Institute for Dental and Craniofacial Sciences, Charité-University Medicine Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
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38
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Kumar S. SWI/SNF (BAF) complexes: From framework to a functional role in endothelial mechanotransduction. CURRENT TOPICS IN MEMBRANES 2021; 87:171-198. [PMID: 34696885 DOI: 10.1016/bs.ctm.2021.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
Endothelial cells (ECs) are constantly subjected to an array of mechanical cues, especially shear stress, due to their luminal placement in the blood vessels. Blood flow can regulate various aspects of endothelial biology and pathophysiology by regulating the endothelial processes at the transcriptomic, proteomic, miRNomic, metabolomics, and epigenomic levels. ECs sense, respond, and adapt to altered blood flow patterns and shear profiles by specialized mechanisms of mechanosensing and mechanotransduction, resulting in qualitative and quantitative differences in their gene expression. Chromatin-regulatory proteins can regulate transcriptional activation by modifying the organization of nucleosomes at promoters, enhancers, silencers, insulators, and locus control regions. Recent research efforts have illustrated that SWI/SNF (SWItch/Sucrose Non-Fermentable) or BRG1/BRM-associated factor (BAF) complex regulates DNA accessibility and chromatin structure. Since the discovery, the gene-regulatory mechanisms of the BAF complex associated with chromatin remodeling have been intensively studied to investigate its role in diverse disease phenotypes. Thus far, it is evident that (1) the SWI/SNF complex broadly regulates the activity of transcriptional enhancers to control lineage-specific differentiation and (2) mutations in the BAF complex proteins lead to developmental disorders and cancers. It is unclear if blood flow can modulate the activity of SWI/SNF complex to regulate EC differentiation and reprogramming. This review emphasizes the integrative role of SWI/SNF complex from a structural and functional standpoint with a special reference to cardiovascular diseases (CVDs). The review also highlights how regulation of this complex by blood flow can lead to the discovery of new therapeutic interventions for the treatment of endothelial dysfunction in vascular diseases.
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Affiliation(s)
- Sandeep Kumar
- Wallace H. Coulter Department of Biomedical Engineering at Emory University and Georgia Institute of Technology, Atlanta, GA, United States.
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39
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Bian E, Chen X, Cheng L, Cheng M, Chen Z, Yue X, Zhang Z, Chen J, Sun L, Huang K, Huang C, Fang Z, Zhao B, Li J. Super-enhancer-associated TMEM44-AS1 aggravated glioma progression by forming a positive feedback loop with Myc. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:337. [PMID: 34696771 PMCID: PMC8543865 DOI: 10.1186/s13046-021-02129-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/05/2021] [Indexed: 01/05/2023]
Abstract
Background Long non-coding RNAs (lncRNAs) have been considered as one type of gene expression regulator for cancer development, but it is not clear how these are regulated. This study aimed to identify a specific lncRNA that promotes glioma progression. Methods RNA sequencing (RNA-seq) and quantitative real-time PCR were performed to screen differentially expressed genes. CCK-8, transwell migration, invasion assays, and a mouse xenograft model were performed to determine the functions of TMEM44-AS1. Co-IP, ChIP, Dual-luciferase reporter assays, RNA pulldown, and RNA immunoprecipitation assays were performed to study the molecular mechanism of TMEM44-AS1 and the downstream target. Results We identified a novel lncRNA TMEM44-AS1, which was aberrantly expressed in glioma tissues, and that increased TMEM44-AS1 expression was correlated with malignant progression and poor survival for patients with glioma. Expression of TMEM44-AS1 increased the proliferation, colony formation, migration, and invasion of glioma cells. Knockdown of TMEM44-AS1 in glioma cells reduced cell proliferation, colony formation, migration and invasion, and tumor growth in a nude mouse xenograft model. Mechanistically, TMEM44-AS1 is directly bound to the SerpinB3, and sequentially activated Myc and EGR1/IL-6 signaling; Myc transcriptionally induced TMEM44-AS1 and directly bound to the promoter and super-enhancer of TMEM44-AS1, thus forming a positive feedback loop with TMEM44-AS. Further studies demonstrated that Myc interacts with MED1 regulates the super-enhancer of TMEM44-AS1. More importantly, a novel small-molecule Myc inhibitor, Myci975, alleviated TMEM44-AS1-promoted the growth of glioma cells. Conclusions Our study implicates a crucial role of the TMEM44-AS1-Myc axis in glioma progression and provides a possible anti-glioma therapeutic agent. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-021-02129-9.
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Affiliation(s)
- Erbao Bian
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China. .,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, 230601, China.
| | - Xueran Chen
- Department of Laboratory Medicine, Hefei Cancer Hospital, Chinese Academy of Sciences, No. 350, Shushan Hu Road, Hefei, 230031, Anhui, China.,Anhui Province Key Laboratory of Medical Physics and Technology; Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, No. 350, Shushan Hu Road, Hefei, 230031, Anhui, China
| | - Li Cheng
- School of pharmacy, Anhui Medical University, Hefei, 230032, China
| | - Meng Cheng
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, 230601, China
| | - Zhigang Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, 230601, China
| | - Xiaoyu Yue
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, 230601, China
| | - Zhengwei Zhang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, 230601, China
| | - Jie Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, 230601, China
| | - Libo Sun
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, 230601, China
| | - Kebing Huang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, 230601, China
| | - Cheng Huang
- School of pharmacy, Anhui Medical University, Hefei, 230032, China
| | - Zhiyou Fang
- Department of Laboratory Medicine, Hefei Cancer Hospital, Chinese Academy of Sciences, No. 350, Shushan Hu Road, Hefei, 230031, Anhui, China. .,Anhui Province Key Laboratory of Medical Physics and Technology; Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, No. 350, Shushan Hu Road, Hefei, 230031, Anhui, China.
| | - Bing Zhao
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China. .,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, 230601, China.
| | - Jun Li
- School of pharmacy, Anhui Medical University, Hefei, 230032, China.
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40
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Chen ZB, Liu X, Chen AT. "Enhancing" mechanosensing: Enhancers and enhancer-derived long non-coding RNAs in endothelial response to flow. CURRENT TOPICS IN MEMBRANES 2021; 87:153-169. [PMID: 34696884 DOI: 10.1016/bs.ctm.2021.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Endothelial cells (ECs), uniquely localized and strategically forming the inner lining of vascular wall, constitute the largest cell surface by area in the human body. The dynamic sensing and response of ECs to mechanical cues, especially shear stress, is crucial for maintenance of vascular homeostasis. It is well recognized that different flow patterns associated with atheroprotective vs atheroprone regions in the arterial tree, result in distinct EC functional phenotypes with differential transcriptome profiles. Mounting evidence has demonstrated an integrative and essential regulatory role of non-coding genome in EC biology. In particular, recent studies have begun to reveal the importance of enhancers and enhancer-derived transcripts in flow-regulated EC gene expression and function. In this minireview, we summarize studies in this area and discuss examples in support of the emerging importance of enhancers and enhancer(-derived) long non-coding RNAs (elncRNAs) in EC mechanosensing, with a focus on flow-responsive EC transcription. Finally, we will provide perspective and discuss standing questions to elucidate the role of these novel regulators in EC mechanobiology.
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Affiliation(s)
- Zhen Bouman Chen
- Department of Diabetes Complications and Metabolism, Duarte, CA, United States; Irell and Manella Graduate School of Biological Sciences, Duarte, CA, United States.
| | - Xuejing Liu
- Department of Diabetes Complications and Metabolism, Duarte, CA, United States
| | - Aleysha T Chen
- Department of Bioengineering, University of California, Berkeley, CA, United States
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41
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Mushimiyimana I, Niskanen H, Beter M, Laakkonen JP, Kaikkonen MU, Ylä-Herttuala S, Laham-Karam N. Characterization of a functional endothelial super-enhancer that regulates ADAMTS18 and angiogenesis. Nucleic Acids Res 2021; 49:8078-8096. [PMID: 34320216 PMCID: PMC8373076 DOI: 10.1093/nar/gkab633] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 05/28/2021] [Accepted: 07/12/2021] [Indexed: 12/20/2022] Open
Abstract
Super-enhancers are clusters of enhancers associated with cell lineage. They can be powerful gene-regulators and may be useful in cell-type specific viral-vector development. Here, we have screened for endothelial super-enhancers and identified an enhancer from within a cluster that conferred 5–70-fold increase in transgene expression. Importantly, CRISPR/Cas9 deletion of enhancers demonstrated regulation of ADAMTS18, corresponding to evidence of chromatin contacts between these genomic regions. Cell division-related pathways were primarily affected by the enhancer deletions, which correlated with significant reduction in cell proliferation. Furthermore, we observed changes in angiogenesis-related genes consistent with the endothelial specificity of this SE. Indeed, deletion of the enhancers affected tube formation, resulting in reduced or shortened sprouts. The super-enhancer angiogenic role is at least partly due to its regulation of ADAMTS18, as siRNA knockdown of ADAMTS18 resulted in significantly shortened endothelial sprouts. Hence, functional characterization of a novel endothelial super-enhancer has revealed substantial downstream effects from single enhancer deletions and led to the discovery of the cis-target gene ADAMTS18 and its role in endothelial function.
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Affiliation(s)
- Isidore Mushimiyimana
- A. I. Virtanen Institute for Molecular Sciences; University of Eastern Finland; Kuopio 70211, Finland
| | - Henri Niskanen
- A. I. Virtanen Institute for Molecular Sciences; University of Eastern Finland; Kuopio 70211, Finland
| | - Mustafa Beter
- A. I. Virtanen Institute for Molecular Sciences; University of Eastern Finland; Kuopio 70211, Finland
| | - Johanna P Laakkonen
- A. I. Virtanen Institute for Molecular Sciences; University of Eastern Finland; Kuopio 70211, Finland
| | - Minna U Kaikkonen
- A. I. Virtanen Institute for Molecular Sciences; University of Eastern Finland; Kuopio 70211, Finland
| | - Seppo Ylä-Herttuala
- A. I. Virtanen Institute for Molecular Sciences; University of Eastern Finland; Kuopio 70211, Finland.,Heart Center and Gene Therapy Unit; Kuopio University Hospital; Kuopio 70029, Finland
| | - Nihay Laham-Karam
- A. I. Virtanen Institute for Molecular Sciences; University of Eastern Finland; Kuopio 70211, Finland
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42
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Strittmatter BG, Jerde TJ, Hollenhorst PC. Ras/ERK and PI3K/AKT signaling differentially regulate oncogenic ERG mediated transcription in prostate cells. PLoS Genet 2021; 17:e1009708. [PMID: 34314419 PMCID: PMC8345871 DOI: 10.1371/journal.pgen.1009708] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 08/06/2021] [Accepted: 07/10/2021] [Indexed: 11/19/2022] Open
Abstract
The TMPRSS2/ERG gene rearrangement occurs in 50% of prostate tumors and results in expression of the transcription factor ERG, which is normally silent in prostate cells. ERG expression promotes prostate tumor formation and luminal epithelial cell fates when combined with PI3K/AKT pathway activation, however the mechanism of synergy is not known. In contrast to luminal fates, expression of ERG alone in immortalized normal prostate epithelial cells promotes cell migration and epithelial to mesenchymal transition (EMT). Migration requires ERG serine 96 phosphorylation via endogenous Ras/ERK signaling. We found that a phosphomimetic mutant, S96E ERG, drove tumor formation and clonogenic survival without activated AKT. S96 was only phosphorylated on nuclear ERG, and differential recruitment of ERK to a subset of ERG-bound chromatin associated with ERG-activated, but not ERG-repressed genes. S96E did not alter ERG genomic binding, but caused a loss of ERG-mediated repression, EZH2 binding and H3K27 methylation. In contrast, AKT activation altered the ERG cistrome and promoted expression of luminal cell fate genes. These data suggest that, depending on AKT status, ERG can promote either luminal or EMT transcription programs, but ERG can promote tumorigenesis independent of these cell fates and tumorigenesis requires only the transcriptional activation function. ERG is the most common oncogene in prostate cancer. The ERG protein can bind DNA and can activate some genes and repress others. Previous studies indicated that ERG cannot promote cancer by itself, but that ERG works together with mutations that activate the protein AKT. In this study we found that activation of AKT changes the genes that ERG regulates, leading to luminal epithelial differentiation, which is a hallmark of most prostate tumors. However, we also found that a mutant version of ERG that can activate, but cannot repress genes, can drive prostate tumorigenesis without activation of AKT, but this mutant ERG cannot promote luminal differentiation. Our findings suggest that ERG mediated tumorigenesis only requires ERG’s activation function and can occur independent of luminal cell differentiation.
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Affiliation(s)
- Brady G. Strittmatter
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, United States of America
| | - Travis J. Jerde
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Peter C. Hollenhorst
- Medical Sciences, Indiana University School of Medicine, Bloomington, Indiana, United States of America
- * E-mail:
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43
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Harada Y, Tanaka T, Arai Y, Isomoto Y, Nakano A, Nakao S, Urasaki A, Watanabe Y, Kawamura T, Nakagawa O. ETS-dependent enhancers for endothelial-specific expression of serum/glucocorticoid-regulated kinase 1 during mouse embryo development. Genes Cells 2021; 26:611-626. [PMID: 34081835 DOI: 10.1111/gtc.12874] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 12/23/2022]
Abstract
Serum/glucocorticoid-regulated kinase 1 (SGK1) is predominantly expressed in endothelial cells of mouse embryos, and Sgk1 null mice show embryonic lethality due to impaired vascular formation. However, how the SGK1 expression is controlled in developing vasculature remains unknown. In this study, we first identified a proximal endothelial enhancer through lacZ reporter mouse analyses. The mouse Sgk1 proximal enhancer was narrowed down to the 5' region of the major transcription initiation site, while a human corresponding region possessed relatively weak activity. We then searched for distal enhancer candidates using in silico analyses of publicly available databases for DNase accessibility, RNA polymerase association and chromatin modification. A region approximately 500 kb distant from the human SGK1 gene was conserved in the mouse, and the mouse and human genomic fragments drove transcription restricted to embryonic endothelial cells. Minimal fragments of both proximal and distal enhancers had consensus binding elements for the ETS transcription factors, which were essential for the responsiveness to ERG, FLI1 and ETS1 proteins in luciferase assays and the endothelial lacZ reporter expression in mouse embryos. These results suggest that endothelial SGK1 expression in embryonic vasculature is maintained through at least two ETS-regulated enhancers located in the proximal and distal regions.
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Affiliation(s)
- Yukihiro Harada
- Department of Molecular Physiology, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan.,Laboratory of Stem Cell & Regenerative Medicine, Department of Biomedical Sciences, College of Life Sciences, Ritsumeikan University, Kusatsu, Japan
| | - Toru Tanaka
- Department of Molecular Physiology, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan
| | - Yuji Arai
- Department of Molecular Physiology, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan.,Laboratory of Animal Experiment and Medical Management, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan
| | - Yoshie Isomoto
- Laboratory of Animal Experiment and Medical Management, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan
| | - Atsushi Nakano
- Laboratory of Animal Experiment and Medical Management, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan
| | - Shu Nakao
- Laboratory of Stem Cell & Regenerative Medicine, Department of Biomedical Sciences, College of Life Sciences, Ritsumeikan University, Kusatsu, Japan
| | - Akihiro Urasaki
- Department of Molecular Physiology, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan
| | - Yusuke Watanabe
- Department of Molecular Physiology, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan
| | - Teruhisa Kawamura
- Laboratory of Stem Cell & Regenerative Medicine, Department of Biomedical Sciences, College of Life Sciences, Ritsumeikan University, Kusatsu, Japan
| | - Osamu Nakagawa
- Department of Molecular Physiology, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan
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44
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Chen B, Zhu Y, Chen J, Feng Y, Xu Y. Activation of TC10-Like Transcription by Lysine Demethylase KDM4B in Colorectal Cancer Cells. Front Cell Dev Biol 2021; 9:617549. [PMID: 34249900 PMCID: PMC8260841 DOI: 10.3389/fcell.2021.617549] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 04/06/2021] [Indexed: 12/19/2022] Open
Abstract
Malignant colorectal cancers (CRCs) are characterized by enhanced migration and invasion thus acquiring the ability to metastasize. We have previously shown that the small GTPase TC10-like (TCL) contributes to aggressive migration and invasion in malignant CRC cells. TCL expression is differentially expressed in CRC cells and can be upregulated by hypoxia although the underlying epigenetic mechanism is not fully appreciated. Here, we report that differential TCL expression in CRC cells appeared to be associated with histone H3K9 methylation. RNAi screening revealed that the lysine demethylase KDM4B was essential for TCL transcription in CRC cells. KDM4B interacted with and was recruited by the sequence-specific transcription factor ETS-related gene 1 (ERG1) to the TCL promoter to activate transcription. Mechanistically, KDM4B mediated H3K9 demethylase facilitated the assembly of pre-initiation complex (PIC) on the TCL promoter. KDM4B knockdown attenuated migration and invasion of CRC cells. Importantly, KDM4B expression was upregulated in human CRC specimens of advanced stages compared to those of lower grades and associated with poor prognosis. Together, these data uncover a novel epigenetic mechanism underlying malignant transformation of CRC cells and suggest that KDM4B may be considered as a therapeutic target in CRC intervention.
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Affiliation(s)
- Baoyu Chen
- Key Laboratory of Targeted Intervention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Yuwen Zhu
- Key Laboratory of Targeted Intervention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Junliang Chen
- Department of Pathophysiology, Wuxi Medical School, Jiangnan University, Wuxi, China
| | - Yifei Feng
- Department of Colorectal Surgery, The First Hospital Affiliated With Nanjing Medical University, Nanjing, China.,Department of General Surgery, The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China
| | - Yong Xu
- Key Laboratory of Targeted Intervention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China.,Institute of Biomedical Research, Liaocheng University, Liaocheng, China
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45
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Quillien A, Gilbert G, Boulet M, Ethuin S, Waltzer L, Vandel L. Prmt5 promotes vascular morphogenesis independently of its methyltransferase activity. PLoS Genet 2021; 17:e1009641. [PMID: 34153034 PMCID: PMC8248709 DOI: 10.1371/journal.pgen.1009641] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 07/01/2021] [Accepted: 06/02/2021] [Indexed: 01/02/2023] Open
Abstract
During development, the vertebrate vasculature undergoes major growth and remodeling. While the transcriptional cascade underlying blood vessel formation starts to be better characterized, little is known concerning the role and mode of action of epigenetic enzymes during this process. Here, we explored the role of the Protein Arginine Methyl Transferase Prmt5 in blood vessel formation as well as hematopoiesis using zebrafish as a model system. Through the combination of different prmt5 loss-of-function approaches we highlighted a key role of Prmt5 in both processes. Notably, we showed that Prmt5 promotes vascular morphogenesis through the transcriptional control of ETS transcription factors and adhesion proteins in endothelial cells. Interestingly, using a catalytic dead mutant of Prmt5 and a specific drug inhibitor, we found that while Prmt5 methyltransferase activity was required for blood cell formation, it was dispensable for vessel formation. Analyses of chromatin architecture impact on reporter genes expression and chromatin immunoprecipitation experiments led us to propose that Prmt5 regulates transcription by acting as a scaffold protein that facilitates chromatin looping to promote vascular morphogenesis. Blood vessel formation is an essential developmental process required for the survival of all vertebrates. The vascular anatomy and the mechanisms involved in vessel formation are highly conserved among vertebrates. Hence, we used zebrafish as a model, to decipher the role and the mode of action of Prmt5, an enzyme known to regulate gene expression, in vascular morphogenesis and in blood cell formation in vivo. Using different approaches, we highlighted a key role of Prmt5 during both processes. However, we found that while blood cell formation required Prmt5 enzymatic activity, vascular morphogenesis was independent on its activity. Prmt5 has been proposed as a therapeutic target in many diseases, including cancer. Yet, we show here that Prmt5 acts at least in part independently of its methyltransferase activity to regulate vascular morphogenesis. By shedding light on a mechanism of action of Prmt5 that will be insensitive to enzymatic inhibitors, our data calls forth the design of alternative drugs. In addition, this non-canonical function of Prmt5 may have a more pervasive role than previously thought in physiological conditions, i.e. during development, but also in pathological situations such as in tumor angiogenesis and certainly deserves more attention in the future.
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Affiliation(s)
- Aurélie Quillien
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
- RESTORE, INSERM UMR1301, CNRS UMR5070, Université Paul Sabatier, Université de Toulouse, Toulouse, France
- * E-mail: (AQ); (LV)
| | - Guerric Gilbert
- Université Clermont Auvergne, CNRS, INSERM, iGReD, Clermont-Ferrand, France
| | - Manon Boulet
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
- Université Clermont Auvergne, CNRS, INSERM, iGReD, Clermont-Ferrand, France
| | - Séverine Ethuin
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Lucas Waltzer
- Université Clermont Auvergne, CNRS, INSERM, iGReD, Clermont-Ferrand, France
| | - Laurence Vandel
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
- Université Clermont Auvergne, CNRS, INSERM, iGReD, Clermont-Ferrand, France
- * E-mail: (AQ); (LV)
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46
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Hong T, Xiao X, Ren J, Cui B, Zong Y, Zou J, Kou Z, Jiang N, Meng G, Zeng G, Shan Y, Wu H, Chen Z, Liang J, Xiao X, Tang J, Wei Y, Ye M, Sun L, Li G, Hu P, Hui R, Zhang H, Wang Y. Somatic MAP3K3 and PIK3CA mutations in sporadic cerebral and spinal cord cavernous malformations. Brain 2021; 144:2648-2658. [PMID: 33729480 DOI: 10.1093/brain/awab117] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/01/2021] [Accepted: 03/07/2021] [Indexed: 01/03/2023] Open
Abstract
Cavernous malformations (CMs) affecting the central nervous system occur in approximately 0.16% to 0.4% of the general population. The majority (85%) of the CMs are in a sporadic form, but the genetic background of sporadic CMs remains enigmatic. Of the 81 patients, 73 (90.1%) patients were detected carrying somatic missense variants in 2 genes: MAP3K3 and PIK3CA by whole-exome sequencing (WES). The mutation spectrum correlated with lesion size (P = 0.001), anatomical distribution (P < 0.001), MRI appearance (P = 0.004) and haemorrhage events (P = 0.006). PIK3CA mutation was a significant predictor of overt haemorrhage events (P = 0.003, OR = 11.252, 95% CI = 2.275-55.648). Enrichment of endothelial cell (EC) population was associated with a higher fractional abundance of the somatic mutations. Overexpression of the MAP3K3 mutation perturbed angiogenesis of EC models in vitro and zebrafish embryos in vivo. Distinct transcriptional signatures between different genetic subgroups of sporadic CMs were identified by single-cell RNA-sequencing (scRNA-seq) and verified by pathological staining. Significant apoptosis in MAP3K3 mutation carriers and overexpression of GDF15 and SERPINA5 in PIK3CA mutation carriers contributed to their phenotype. We identified activating MAP3K3 and PIK3CA somatic mutations in the majority (90.1%) of sporadic CMs and PIK3CA mutations could confer a higher risk for overt haemorrhage. Our data provide insights into genomic landscapes, propose a mechanistic explanation and underscore the possibility of a molecular classification for sporadic CMs.
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Affiliation(s)
- Tao Hong
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, China International Neuroscience Institute, Beijing, China
| | - Xiao Xiao
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jian Ren
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, China International Neuroscience Institute, Beijing, China
| | - Bing Cui
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuru Zong
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jian Zou
- The Institute of Translational Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Zqi Kou
- The Institute of Translational Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Nan Jiang
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, China International Neuroscience Institute, Beijing, China
| | - Guolu Meng
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, China International Neuroscience Institute, Beijing, China
| | - Gao Zeng
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, China International Neuroscience Institute, Beijing, China
| | - Yongzhi Shan
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, China International Neuroscience Institute, Beijing, China
| | - Hao Wu
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, China International Neuroscience Institute, Beijing, China
| | - Zan Chen
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, China International Neuroscience Institute, Beijing, China
| | - Jiantao Liang
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, China International Neuroscience Institute, Beijing, China
| | - Xinru Xiao
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, China International Neuroscience Institute, Beijing, China
| | - Jie Tang
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, China International Neuroscience Institute, Beijing, China
| | - Yukui Wei
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, China International Neuroscience Institute, Beijing, China
| | - Ming Ye
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, China International Neuroscience Institute, Beijing, China
| | - Liyong Sun
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, China International Neuroscience Institute, Beijing, China
| | - Guilin Li
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, China International Neuroscience Institute, Beijing, China
| | - Peng Hu
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, China International Neuroscience Institute, Beijing, China
| | - Rutai Hui
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hongqi Zhang
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, China International Neuroscience Institute, Beijing, China
| | - Yibo Wang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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47
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Bauer S, Ratz L, Heckmann-Nötzel D, Kaczorowski A, Hohenfellner M, Kristiansen G, Duensing S, Altevogt P, Klauck SM, Sültmann H. miR-449a Repression Leads to Enhanced NOTCH Signaling in TMPRSS2:ERG Fusion Positive Prostate Cancer Cells. Cancers (Basel) 2021; 13:964. [PMID: 33669024 PMCID: PMC7975324 DOI: 10.3390/cancers13050964] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 02/18/2021] [Accepted: 02/18/2021] [Indexed: 12/24/2022] Open
Abstract
About 50% of prostate cancer (PCa) tumors are TMPRSS2:ERG (T2E) fusion-positive (T2E+), but the role of T2E in PCa progression is not fully understood. We were interested in investigating epigenomic alterations associated with T2E+ PCa. Using different sequencing cohorts, we found several transcripts of the miR-449 cluster to be repressed in T2E+ PCa. This repression correlated strongly with enhanced expression of NOTCH and several of its target genes in TCGA and ICGC PCa RNA-seq data. We corroborated these findings using a cellular model with inducible T2E expression. Overexpression of miR-449a in vitro led to silencing of genes associated with NOTCH signaling (NOTCH1, HES1) and HDAC1. Interestingly, HDAC1 overexpression led to the repression of HES6, a negative regulator of the transcription factor HES1, the primary effector of NOTCH signaling, and promoted cell proliferation by repressing the cell cycle inhibitor p21. Inhibition of NOTCH as well as knockdown of HES1 reduced the oncogenic properties of PCa cell lines. Using tissue microarray analysis encompassing 533 human PCa cores, ERG-positive areas exhibited significantly increased HES1 expression. Taken together, our data suggest that an epigenomic regulatory network enhances NOTCH signaling and thereby contributes to the oncogenic properties of T2E+ PCa.
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Affiliation(s)
- Simone Bauer
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany; (S.B.); (D.H.-N.); (S.M.K.)
- Medical Faculty, Heidelberg University, 69120 Heidelberg, Germany
| | - Leonie Ratz
- Department of Obstetrics and Gynecology, University Hospital of Cologne, 50937 Cologne, Germany;
| | - Doreen Heckmann-Nötzel
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany; (S.B.); (D.H.-N.); (S.M.K.)
- Computer Assisted Medical Interventions, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Adam Kaczorowski
- Molecular Urooncology, Department of Urology, University Hospital Heidelberg, 69120 Heidelberg, Germany; (A.K.); (S.D.)
| | - Markus Hohenfellner
- Department of Urology, University Hospital Heidelberg and National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany;
| | - Glen Kristiansen
- Center for Integrated Oncology, Institute of Pathology, University of Bonn, 53127 Bonn, Germany;
| | - Stefan Duensing
- Molecular Urooncology, Department of Urology, University Hospital Heidelberg, 69120 Heidelberg, Germany; (A.K.); (S.D.)
- Department of Urology, University Hospital Heidelberg and National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany;
| | - Peter Altevogt
- Skin Cancer Unit, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany;
- Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim, Germany
| | - Sabine M. Klauck
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany; (S.B.); (D.H.-N.); (S.M.K.)
| | - Holger Sültmann
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany; (S.B.); (D.H.-N.); (S.M.K.)
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48
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Yao LL, Hu JX, Li Q, Lee D, Ren X, Zhang JS, Sun D, Zhang HS, Wang YG, Mei L, Xiong WC. Astrocytic neogenin/netrin-1 pathway promotes blood vessel homeostasis and function in mouse cortex. J Clin Invest 2021; 130:6490-6509. [PMID: 32853179 DOI: 10.1172/jci132372] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 08/20/2020] [Indexed: 12/14/2022] Open
Abstract
Astrocytes have multiple functions in the brain, including affecting blood vessel (BV) homeostasis and function. However, the underlying mechanisms remain elusive. Here, we provide evidence that astrocytic neogenin (NEO1), a member of deleted in colorectal cancer (DCC) family netrin receptors, is involved in blood vessel homeostasis and function. Mice with Neo1 depletion in astrocytes exhibited clustered astrocyte distribution and increased BVs in their cortices. These BVs were leaky, with reduced blood flow, disrupted vascular basement membranes (vBMs), decreased pericytes, impaired endothelial cell (EC) barrier, and elevated tip EC proliferation. Increased proliferation was also detected in cultured ECs exposed to the conditioned medium (CM) of NEO1-depleted astrocytes. Further screening for angiogenetic factors in the CM identified netrin-1 (NTN1), whose expression was decreased in NEO1-depleted cortical astrocytes. Adding NTN1 into the CM of NEO1-depleted astrocytes attenuated EC proliferation. Expressing NTN1 in NEO1 mutant cortical astrocytes ameliorated phenotypes in blood-brain barrier (BBB), EC, and astrocyte distribution. NTN1 depletion in astrocytes resulted in BV/BBB deficits in the cortex similar to those in Neo1 mutant mice. In aggregate, these results uncovered an unrecognized pathway, astrocytic NEO1 to NTN1, not only regulating astrocyte distribution, but also promoting cortical BV homeostasis and function.
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Affiliation(s)
- Ling-Ling Yao
- Department of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA.,Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, Georgia, USA
| | - Jin-Xia Hu
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, Georgia, USA.,Institute of Stroke Center and Department of Neurology, Xuzhou Medical University, The Affiliated Hospital of Xuzhou Medical University, Jiangsu, China
| | - Qiang Li
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, Georgia, USA.,Department of Hand Surgery, China-Japan Union Hospital, Jilin University, Changchun, China
| | - Daehoon Lee
- Department of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Xiao Ren
- Department of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA.,Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jun-Shi Zhang
- Department of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA.,Department of Neurology, Huaihe Hospital, Henan University, Kaifeng, Henan, China
| | - Dong Sun
- Department of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA.,Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, Georgia, USA
| | - Hong-Sheng Zhang
- Department of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA.,Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, Georgia, USA
| | - Yong-Gang Wang
- Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Lin Mei
- Department of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA.,Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, Georgia, USA
| | - Wen-Cheng Xiong
- Department of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA.,Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, Georgia, USA
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49
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Endothelial ERG alleviates cardiac fibrosis via blocking endothelin-1-dependent paracrine mechanism. Cell Biol Toxicol 2021; 37:873-890. [PMID: 33469864 DOI: 10.1007/s10565-021-09581-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 01/07/2021] [Indexed: 12/12/2022]
Abstract
Cardiac endothelium communicates closely with adjacent cardiac cells by multiple cytokines and plays critical roles in regulating fibroblasts proliferation, activation, and collagen synthesis during cardiac fibrosis. E26 transformation-specific (ETS)-related gene (ERG) belongs to the ETS transcriptional factor family and is required for endothelial cells (ECs) homeostasis and cardiac development. This study aims at investigating the potential role and molecular basis of ERG in fibrotic remodeling within the adult heart. We observed that ERG was abundant in murine hearts, especially in cardiac ECs, but decreased during cardiac fibrosis. ERG knockdown within murine hearts caused spontaneously cardiac fibrosis and dysfunction, accompanied by the activation of multiple Smad-dependent and independent pathways. However, the direct silence of ERG in cardiac fibroblasts did not affect the expression of fibrotic markers. Intriguingly, ERG knockdown in human umbilical vein endothelial cells (HUVECs) promoted the secretion of endothelin-1 (ET-1), which subsequently accelerated the proliferation, phenotypic transition, and collagen synthesis of cardiac fibroblasts in a paracrine manner. Suppressing ET-1 with either a neutralizing antibody or a receptor blocker abolished ERG knockdown-mediated deleterious effect in vivo and in vitro. This pro-fibrotic effect was also negated by RGD (Arg-Gly-Asp)-peptide magnetic nanoparticles target delivery of ET-1 small interfering RNA to ECs in mice. More importantly, we proved that endothelial ERG overexpression notably prevented pressure overload-induced cardiac fibrosis. Collectively, endothelial ERG alleviates cardiac fibrosis via blocking ET-1-dependent paracrine mechanism and it functions as a candidate for treating cardiac fibrosis. • ERG is abundant in murine hearts, especially in cardiac ECs, but decreased during fibrotic remodeling. • ERG knockdown causes spontaneously cardiac fibrosis and dysfunction. • ERG silence in HUVECs promotes the secretion of endothelin-1, which in turn activates cardiac fibroblasts in a paracrine manner. • Endothelial ERG overexpression prevents pressure overload-induced cardiac fibrosis.
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50
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Neal A, Nornes S, Louphrasitthiphol P, Sacilotto N, Preston MD, Fleisinger L, Payne S, De Val S. ETS factors are required but not sufficient for specific patterns of enhancer activity in different endothelial subtypes. Dev Biol 2021; 473:1-14. [PMID: 33453264 PMCID: PMC8026812 DOI: 10.1016/j.ydbio.2021.01.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 12/16/2020] [Accepted: 01/08/2021] [Indexed: 12/11/2022]
Abstract
Correct vascular differentiation requires distinct patterns of gene expression in different subtypes of endothelial cells. Members of the ETS transcription factor family are essential for the transcriptional activation of arterial and angiogenesis-specific gene regulatory elements, leading to the hypothesis that they play lineage-defining roles in arterial and angiogenic differentiation directly downstream of VEGFA signalling. However, an alternative explanation is that ETS binding at enhancers and promoters is a general requirement for activation of many endothelial genes regardless of expression pattern, with subtype-specificity provided by additional factors. Here we use analysis of Ephb4 and Coup-TFII (Nr2f2) vein-specific enhancers to demonstrate that ETS factors are equally essential for vein, arterial and angiogenic-specific enhancer activity patterns. Further, we show that ETS factor binding at these vein-specific enhancers is enriched by VEGFA signalling, similar to that seen at arterial and angiogenic enhancers. However, while arterial and angiogenic enhancers can be activated by VEGFA in vivo, the Ephb4 and Coup-TFII venous enhancers are not, suggesting that the specificity of VEGFA-induced arterial and angiogenic enhancer activity occurs via non-ETS transcription factors. These results support a model in which ETS factors are not the primary regulators of specific patterns of gene expression in different endothelial subtypes. Vein-specific enhancers can contain essential ETS motifs. VEGFA induced an increase in ETS binding at vein, arterial and angiogenic enhancers. VEGFA stimulation cannot induce vein-specific enhancer activity.
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Affiliation(s)
- Alice Neal
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, United Kingdom.
| | - Svanhild Nornes
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, United Kingdom
| | - Pakavarin Louphrasitthiphol
- Ludwig Institute for Cancer Research Ltd, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, United Kingdom
| | - Natalia Sacilotto
- Ludwig Institute for Cancer Research Ltd, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, United Kingdom
| | - Mark D Preston
- National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, EN6 3QG, United Kingdom
| | - Lucija Fleisinger
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, United Kingdom
| | - Sophie Payne
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, United Kingdom; Ludwig Institute for Cancer Research Ltd, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, United Kingdom
| | - Sarah De Val
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, United Kingdom; Ludwig Institute for Cancer Research Ltd, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, United Kingdom.
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