1
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Zhang J. Non-coding RNAs and angiogenesis in cardiovascular diseases: a comprehensive review. Mol Cell Biochem 2024:10.1007/s11010-023-04919-5. [PMID: 38306012 DOI: 10.1007/s11010-023-04919-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 12/18/2023] [Indexed: 02/03/2024]
Abstract
Non-coding RNAs (ncRNAs) have key roles in the etiology of many illnesses, including heart failure, myocardial infarction, stroke, and in physiological processes like angiogenesis. In transcriptional regulatory circuits that control heart growth, signaling, and stress response, as well as remodeling in cardiac disease, ncRNAs have become important players. Studies on ncRNAs and cardiovascular disease have made great progress recently. Here, we go through the functions of non-coding RNAs (ncRNAs) like circular RNAs (circRNAs), and microRNAs (miRNAs) as well as long non-coding RNAs (lncRNAs) in modulating cardiovascular disorders.
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Affiliation(s)
- Jie Zhang
- Medical School, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China.
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2
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Xie Y, Peng X, Li P. MIWE: detecting the critical states of complex biological systems by the mutual information weighted entropy. BMC Bioinformatics 2024; 25:44. [PMID: 38280998 PMCID: PMC10822190 DOI: 10.1186/s12859-024-05667-z] [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: 12/07/2023] [Accepted: 01/22/2024] [Indexed: 01/29/2024] Open
Abstract
Complex biological systems often undergo sudden qualitative changes during their dynamic evolution. These critical transitions are typically characterized by a catastrophic progression of the system. Identifying the critical point is critical to uncovering the underlying mechanisms of complex biological systems. However, the system may exhibit minimal changes in its state until the critical point is reached, and in the face of high throughput and strong noise data, traditional biomarkers may not be effective in distinguishing the critical state. In this study, we propose a novel approach, mutual information weighted entropy (MIWE), which uses mutual information between genes to build networks and identifies critical states by quantifying molecular dynamic differences at each stage through weighted differential entropy. The method is applied to one numerical simulation dataset and four real datasets, including bulk and single-cell expression datasets. The critical states of the system can be recognized and the robustness of MIWE method is verified by numerical simulation under the influence of different noises. Moreover, we identify two key transcription factors (TFs), CREB1 and CREB3, that regulate downstream signaling genes to coordinate cell fate commitment. The dark genes in the single-cell expression datasets are mined to reveal the potential pathway regulation mechanism.
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Affiliation(s)
- Yuke Xie
- School of Mathematics and Statistics, Henan University of Science and Technology, Luoyang, 471000, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
| | - Xueqing Peng
- School of Mathematics and Statistics, Henan University of Science and Technology, Luoyang, 471000, China
| | - Peiluan Li
- School of Mathematics and Statistics, Henan University of Science and Technology, Luoyang, 471000, China.
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3
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Das S, Gupta V, Bjorge J, Shi X, Gong W, Garry MG, Garry DJ. ETV2 and VEZF1 interaction and regulation of the hematoendothelial lineage during embryogenesis. Front Cell Dev Biol 2023; 11:1109648. [PMID: 36923254 PMCID: PMC10009235 DOI: 10.3389/fcell.2023.1109648] [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: 11/28/2022] [Accepted: 02/13/2023] [Indexed: 03/02/2023] Open
Abstract
Ets variant 2 (Etv2), a member of the Ets factor family, has an essential role in the formation of endothelial and hematopoietic cell lineages during embryonic development. The functional role of ETS transcription factors is, in part, dependent on the interacting proteins. There are relatively few studies exploring the coordinated interplay between ETV2 and its interacting proteins that regulate mesodermal lineage determination. In order to identify novel ETV2 interacting partners, a yeast two-hybrid analysis was performed and the C2H2 zinc finger transcription factor VEZF1 (vascular endothelial zinc finger 1) was identified as a binding factor, which was specifically expressed within the endothelium during vascular development. To confirm this interaction, co-immunoprecipitation and GST pull down assays demonstrated the direct interaction between ETV2 and VEZF1. During embryoid body differentiation, Etv2 achieved its peak expression at day 3.0 followed by rapid downregulation, on the other hand Vezf1 expression increased through day 6 of EB differentiation. We have previously shown that ETV2 potently activated Flt1 gene transcription. Using a Flt1 promoter-luciferase reporter assay, we demonstrated that VEZF1 co-activated the Flt1 promoter. Electrophoretic mobility shift assay and Chromatin immunoprecipitation established VEZF1 binding to the Flt1 promoter. Vezf1 knockout embryonic stem cells had downregulation of hematoendothelial marker genes when undergoing embryoid body mediated mesodermal differentiation whereas overexpression of VEZF1 induced the expression of hematoendothelial genes during differentiation. These current studies provide insight into the co-regulation of the hemato-endothelial lineage development via a co-operative interaction between ETV2 and VEZF1.
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Affiliation(s)
- Satyabrata Das
- Department of Medicine, Cardiovascular Division, Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, United States
| | - Vinayak Gupta
- Department of Medicine, Cardiovascular Division, Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, United States
| | - Johannes Bjorge
- Department of Medicine, Cardiovascular Division, Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, United States
| | - Xiaozhong Shi
- Department of Physiology, Basic Medical College, Nanchang University, Nanchang, JX, China
| | - Wuming Gong
- Department of Medicine, Cardiovascular Division, Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, United States
| | - Mary G. Garry
- Department of Medicine, Cardiovascular Division, Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, United States
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, United States
- Paul and Sheila Wellstone Muscular Dystrophy Center, University of Minnesota, Minneapolis, MN, United States
| | - Daniel J. Garry
- Department of Medicine, Cardiovascular Division, Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, United States
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, United States
- Paul and Sheila Wellstone Muscular Dystrophy Center, University of Minnesota, Minneapolis, MN, United States
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4
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Mungale A, McGaughey DM, Zhang C, Yousaf S, Liu J, Brooks BP, Maminishkis A, Fufa TD, Hufnagel RB. Transcriptional mapping of the macaque retina and RPE-choroid reveals conserved inter-tissue transcription drivers and signaling pathways. Front Genet 2022; 13:949449. [PMID: 36506320 PMCID: PMC9732541 DOI: 10.3389/fgene.2022.949449] [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: 05/21/2022] [Accepted: 11/01/2022] [Indexed: 11/27/2022] Open
Abstract
The macula and fovea comprise a highly sensitive visual detection tissue that is susceptible to common disease processes like age-related macular degeneration (AMD). Our understanding of the molecular determinants of high acuity vision remains unclear, as few model organisms possess a human-like fovea. We explore transcription factor networks and receptor-ligand interactions to elucidate tissue interactions in the macula and peripheral retina and concomitant changes in the underlying retinal pigment epithelium (RPE)/choroid. Poly-A selected, 100 bp paired-end RNA-sequencing (RNA-seq) was performed across the macular/foveal, perimacular, and temporal peripheral regions of the neural retina and RPE/choroid tissues of four adult Rhesus macaque eyes to characterize region- and tissue-specific gene expression. RNA-seq reads were mapped to both the macaque and human genomes for maximum alignment and analyzed for differential expression and Gene Ontology (GO) enrichment. Comparison of the neural retina and RPE/choroid tissues indicated distinct, contiguously changing gene expression profiles from fovea through perimacula to periphery. Top GO enrichment of differentially expressed genes in the RPE/choroid included cell junction organization and epithelial cell development. Expression of transcriptional regulators and various disease-associated genes show distinct location-specific preference and retina-RPE/choroid tissue-tissue interactions. Regional gene expression changes in the macaque retina and RPE/choroid is greater than that found in previously published transcriptome analysis of the human retina and RPE/choroid. Further, conservation of human macula-specific transcription factor profiles and gene expression in macaque tissues suggest a conservation of programs required for retina and RPE/choroid function and disease susceptibility.
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Affiliation(s)
- Ameera Mungale
- Medical Genetics and Ophthalmic Genomics Unit, National Eye Institute, National Institutes of Health, Bethesda, MD, United States
| | - David M. McGaughey
- Bioinformatics Group, National Eye Institute, National Institutes of Health, Bethesda, MD, United States
| | - Congxiao Zhang
- Section on Epithelial and Retinal Physiology and Disease, National Eye Institute, National Institutes of Health, Bethesda, MD, United States
| | - Sairah Yousaf
- Medical Genetics and Ophthalmic Genomics Unit, National Eye Institute, National Institutes of Health, Bethesda, MD, United States
| | - James Liu
- Medical Genetics and Ophthalmic Genomics Unit, National Eye Institute, National Institutes of Health, Bethesda, MD, United States
| | - Brian P. Brooks
- Pediatric, Developmental and Genetic Ophthalmology, National Eye Institute, National Institutes of Health, Bethesda, MD, United States
| | - Arvydas Maminishkis
- Section on Epithelial and Retinal Physiology and Disease, National Eye Institute, National Institutes of Health, Bethesda, MD, United States
| | - Temesgen D. Fufa
- Medical Genetics and Ophthalmic Genomics Unit, National Eye Institute, National Institutes of Health, Bethesda, MD, United States
| | - Robert B. Hufnagel
- Medical Genetics and Ophthalmic Genomics Unit, National Eye Institute, National Institutes of Health, Bethesda, MD, United States,*Correspondence: Robert B. Hufnagel,
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5
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Chen H, Zhang M, Zhang J, Chen Y, Zuo Y, Xie Z, Zhou G, Chen S, Chen Y. Application of Induced Pluripotent Stem Cell-Derived Models for Investigating microRNA Regulation in Developmental Processes. Front Genet 2022; 13:899831. [PMID: 35719367 PMCID: PMC9204592 DOI: 10.3389/fgene.2022.899831] [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: 03/19/2022] [Accepted: 05/06/2022] [Indexed: 11/29/2022] Open
Abstract
Advances in induced pluripotent stem cell (iPSC) techniques have opened up new perspectives in research on developmental biology. Compared with other sources of human cellular models, iPSCs present a great advantage in hosting the unique genotype background of donors without ethical concerns. A wide spectrum of cellular and organoid models can be generated from iPSCs under appropriate in vitro conditions. The pluripotency of iPSCs is orchestrated by external signalling and regulated at the epigenetic, transcriptional and posttranscriptional levels. Recent decades have witnessed the progress of studying tissue-specific expressions and functions of microRNAs (miRNAs) using iPSC-derived models. MiRNAs are a class of short non-coding RNAs with regulatory functions in various biological processes during development, including cell migration, proliferation and apoptosis. MiRNAs are key modulators of gene expression and promising candidates for biomarker in development; hence, research on the regulation of human development by miRNAs is expanding. In this review, we summarize the current progress in the application of iPSC-derived models to studies of the regulatory roles of miRNAs in developmental processes.
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Affiliation(s)
- Hongyu Chen
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Mimi Zhang
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jingzhi Zhang
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yapei Chen
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yabo Zuo
- Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, China
| | - Zhishen Xie
- Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, China
| | - Guanqing Zhou
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shehong Chen
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yaoyong Chen
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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6
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Zhao P, Xu S, Huang Z, Deng P, Zhang Y. Identify specific gene pairs for subarachnoid hemorrhage based on wavelet analysis and genetic algorithm. PLoS One 2021; 16:e0253219. [PMID: 34138931 PMCID: PMC8211192 DOI: 10.1371/journal.pone.0253219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 05/29/2021] [Indexed: 11/18/2022] Open
Abstract
Subarachnoid hemorrhage (SAH) is a fatal stroke caused by bleeding in the brain. SAH can be caused by a ruptured aneurysm or head injury. One-third of patients will survive and recover. One-third will survive with disability; one-third will die. The focus of treatment is to stop bleeding, restore normal blood flow, and prevent vasospasm. Treatment for SAH varies, depending on the bleeding’s underlying cause and the extent of damage to the brain. Treatment may include lifesaving measures, symptom relief, repair of the bleeding vessel, and complication prevention. However, the useful diagnostic biomarkers of SAH are still limited due to the instability of gene marker expression. To overcome this limitation, we developed a new protocol pairing genes and screened significant gene pairs based on the feature selection algorithm. A classifier was constructed with the selected gene pairs and achieved a high performance.
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Affiliation(s)
- Pengcheng Zhao
- Department of Neurosurgery, Anhui No. 2 Provincal People’s Hospital, Hefei, Anhui, China
| | - Shaonian Xu
- Department of Neurosurgery, Anhui No. 2 Provincal People’s Hospital, Hefei, Anhui, China
| | - Zhenshan Huang
- Department of Neurosurgery, Anhui No. 2 Provincal People’s Hospital, Hefei, Anhui, China
| | - Pengcheng Deng
- Department of Neurosurgery, Anhui No. 2 Provincal People’s Hospital, Hefei, Anhui, China
| | - Yongming Zhang
- Department of Neurosurgery, Anhui No. 2 Provincal People’s Hospital, Hefei, Anhui, China
- * E-mail:
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7
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Paavola J, Alakoski T, Ulvila J, Kilpiö T, Sirén J, Perttunen S, Narumanchi S, Wang H, Lin R, Porvari K, Junttila J, Huikuri H, Immonen K, Lakkisto P, Magga J, Tikkanen I, Kerkelä R. Vezf1 regulates cardiac structure and contractile function. EBioMedicine 2020; 51:102608. [PMID: 31911272 PMCID: PMC6948172 DOI: 10.1016/j.ebiom.2019.102608] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 12/10/2019] [Accepted: 12/13/2019] [Indexed: 11/30/2022] Open
Abstract
Background Vascular endothelial zinc finger 1 (Vezf1) is a transcription factor previously shown to regulate vasculogenesis and angiogenesis. We aimed to investigate the role of Vezf1 in the postnatal heart. Methods The role of Vezf1 in regulating cardiac growth and contractile function was studied in zebrafish and in primary cardiomyocytes. Findings We find that expression of Vezf1 is decreased in diseased human myocardium and mouse hearts. Our experimental data shows that knockdown of zebrafish Vezf1 reduces cardiac growth and results in impaired ventricular contractile response to β-adrenergic stimuli. However, Vezf1 knockdown is not associated with dysregulation of cardiomyocyte Ca2+ transient kinetics. Gene ontology enrichment analysis indicates that Vezf1 regulates cardiac muscle contraction and dilated cardiomyopathy related genes and we identify cardiomyocyte Myh7/β-MHC as key target for Vezf1. We further identify a key role for an MCAT binding site in the Myh7 promoter regulating the response to Vezf1 knockdown and show that TEAD-1 is a binding partner of Vezf1. Interpretation We demonstrate a role for Vezf1 in regulation of compensatory cardiac growth and cardiomyocyte contractile function, which may be relevant in human cardiac disease.
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Affiliation(s)
- Jere Paavola
- Unit of Cardiovascular Research, Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Tarja Alakoski
- Research Unit of Biomedicine, Department of Pharmacology and Toxicology, University of Oulu, Finland
| | - Johanna Ulvila
- Research Unit of Biomedicine, Department of Pharmacology and Toxicology, University of Oulu, Finland
| | - Teemu Kilpiö
- Research Unit of Biomedicine, Department of Pharmacology and Toxicology, University of Oulu, Finland; Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Juuso Sirén
- Unit of Cardiovascular Research, Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Sanni Perttunen
- Unit of Cardiovascular Research, Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Suneeta Narumanchi
- Unit of Cardiovascular Research, Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Hong Wang
- Unit of Cardiovascular Research, Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Ruizhu Lin
- Research Unit of Biomedicine, Department of Pharmacology and Toxicology, University of Oulu, Finland; Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Katja Porvari
- Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland; Department of Forensic Medicine, Research Unit of Internal Medicine, University of Oulu, Oulu, Finland
| | - Juhani Junttila
- Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland; Division of Cardiology, Research Unit of Internal Medicine, University of Oulu and Oulu University Hospital, Oulu, Finland
| | - Heikki Huikuri
- Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland; Division of Cardiology, Research Unit of Internal Medicine, University of Oulu and Oulu University Hospital, Oulu, Finland
| | - Katariina Immonen
- Unit of Cardiovascular Research, Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Päivi Lakkisto
- Unit of Cardiovascular Research, Minerva Foundation Institute for Medical Research, Helsinki, Finland; Clinical Chemistry and Hematology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Johanna Magga
- Research Unit of Biomedicine, Department of Pharmacology and Toxicology, University of Oulu, Finland
| | - Ilkka Tikkanen
- Unit of Cardiovascular Research, Minerva Foundation Institute for Medical Research, Helsinki, Finland; Abdominal Center, Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Risto Kerkelä
- Research Unit of Biomedicine, Department of Pharmacology and Toxicology, University of Oulu, Finland; Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland.
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8
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Du K, Zhao C, Wang L, Wang Y, Zhang KZ, Shen XY, Sun HX, Gao W, Lu X. MiR-191 inhibit angiogenesis after acute ischemic stroke targeting VEZF1. Aging (Albany NY) 2019; 11:2762-2786. [PMID: 31064890 PMCID: PMC6535071 DOI: 10.18632/aging.101948] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 04/29/2019] [Indexed: 04/13/2023]
Abstract
Acute ischemic stroke (AIS) is a major public health problem in China. Impaired angiogenesis plays crucial roles in the development of ischemic cerebral injury. Recent studies have identified that microRNAs (miRNAs) are important regulators of angiogenesis, but little is known the exact effects of angiogenesis-associated miRNAs in AIS. In the present study, we detected the expression levels of angiogenesis-associated miRNAs in AIS patients, middle cerebral artery occlusion (MCAO) rats, and oxygen-glucose deprivation/reoxygenation (OGD/R) human umbilical vein endothelial cells (HUVECs). MiR-191 was increased in the plasma of AIS patients, OGD/R HUVECs, and the plasma and brain of MCAO rats. Over-expression of miR-191 promoted apoptosis, but reduced the proliferation, migration, tube-forming and spheroid sprouting activity in HUVECs OGD/R model. Mechanically, vascular endothelial zinc finger 1 (VEZF1) was identified as the direct target of miR-191, and could be regulated by miR-191 at post-translational level. In vivo studies applying miR-191 antagomir demonstrated that inhibition of miR-191 reduced infarction volume in MCAO rats. In conclusion, our data reveal a novel role of miR-191 in promoting ischemic brain injury through inhibiting angiogenesis via targeting VEZF1. Therefore, miR-191 may serve as a biomarker or a therapeutic target for AIS.
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Affiliation(s)
- Kang Du
- Department of Geriatrics, Sir Run Run Hospital, Nanjing Medical University, Nanjing 211166, Jiangsu Province, China
- Key Laboratory for Aging and Disease, Nanjing Medical University, Nanjing 211166, Jiangsu Province, China
- Equal contribution
| | - Can Zhao
- Department of Geriatrics, Sir Run Run Hospital, Nanjing Medical University, Nanjing 211166, Jiangsu Province, China
- Key Laboratory for Aging and Disease, Nanjing Medical University, Nanjing 211166, Jiangsu Province, China
- Equal contribution
| | - Li Wang
- Department of Geriatrics, Sir Run Run Hospital, Nanjing Medical University, Nanjing 211166, Jiangsu Province, China
- Key Laboratory for Aging and Disease, Nanjing Medical University, Nanjing 211166, Jiangsu Province, China
| | - Yue Wang
- Department of Geriatrics, Sir Run Run Hospital, Nanjing Medical University, Nanjing 211166, Jiangsu Province, China
- Key Laboratory for Aging and Disease, Nanjing Medical University, Nanjing 211166, Jiangsu Province, China
| | - Kang-Zhen Zhang
- Department of Geriatrics, Sir Run Run Hospital, Nanjing Medical University, Nanjing 211166, Jiangsu Province, China
- Key Laboratory for Aging and Disease, Nanjing Medical University, Nanjing 211166, Jiangsu Province, China
| | - Xi-Yu Shen
- Department of Geriatrics, Sir Run Run Hospital, Nanjing Medical University, Nanjing 211166, Jiangsu Province, China
- Key Laboratory for Aging and Disease, Nanjing Medical University, Nanjing 211166, Jiangsu Province, China
| | - Hui-Xian Sun
- Department of Geriatrics, Sir Run Run Hospital, Nanjing Medical University, Nanjing 211166, Jiangsu Province, China
- Key Laboratory for Aging and Disease, Nanjing Medical University, Nanjing 211166, Jiangsu Province, China
| | - Wei Gao
- Department of Geriatrics, Sir Run Run Hospital, Nanjing Medical University, Nanjing 211166, Jiangsu Province, China
- Key Laboratory for Aging and Disease, Nanjing Medical University, Nanjing 211166, Jiangsu Province, China
| | - Xiang Lu
- Department of Geriatrics, Sir Run Run Hospital, Nanjing Medical University, Nanjing 211166, Jiangsu Province, China
- Key Laboratory for Aging and Disease, Nanjing Medical University, Nanjing 211166, Jiangsu Province, China
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9
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Characterization of Small Molecules Inhibiting the Pro-Angiogenic Activity of the Zinc Finger Transcription Factor Vezf1. Molecules 2018; 23:molecules23071615. [PMID: 29970794 PMCID: PMC6100598 DOI: 10.3390/molecules23071615] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 06/23/2018] [Accepted: 06/24/2018] [Indexed: 02/01/2023] Open
Abstract
Discovery of inhibitors for endothelial-related transcription factors can contribute to the development of anti-angiogenic therapies that treat various diseases, including cancer. The role of transcription factor Vezf1 in vascular development and regulation of angiogenesis has been defined by several earlier studies. Through construction of a computational model for Vezf1, work here has identified a novel small molecule drug capable of inhibiting Vezf1 from binding to its cognate DNA binding site. Using structure-based design and virtual screening of the NCI Diversity Compound Library, 12 shortlisted compounds were tested for their ability to interfere with the binding of Vezf1 to DNA using electrophoretic gel mobility shift assays. We identified one compound, T4, which has an IC50 of 20 μM. Using murine endothelial cells, MSS31, we tested the effect of T4 on endothelial cell viability and angiogenesis by using tube formation assay. Our data show that addition of T4 in cell culture medium does not affect cell viability at concentrations lower or equal to its IC 50 but strongly inhibits the network formation by MSS31 in the tube formation assays. Given its potential efficacy, this inhibitor has significant therapeutic potential in several human diseases.
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10
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AlAbdi L, He M, Yang Q, Norvil AB, Gowher H. The transcription factor Vezf1 represses the expression of the antiangiogenic factor Cited2 in endothelial cells. J Biol Chem 2018; 293:11109-11118. [PMID: 29794136 PMCID: PMC6052231 DOI: 10.1074/jbc.ra118.002911] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 05/19/2018] [Indexed: 01/05/2023] Open
Abstract
Formation of the vasculature by angiogenesis is critical for proper development, but angiogenesis also contributes to the pathogenesis of various disorders, including cancer and cardiovascular diseases. Vascular endothelial zinc finger 1 (Vezf1), is a Krüppel-like zinc finger protein that plays a vital role in vascular development. However, the mechanism by which Vezf1 regulates this process is not fully understood. Here, we show that Vezf1−/− mouse embryonic stem cells (ESC) have significantly increased expression of a stem cell factor, Cbp/p300-interacting transactivator 2 (Cited2). Compared with WT ESCs, Vezf1−/− ESCs inefficiently differentiated into endothelial cells (ECs), which exhibited defects in the tube-formation assay. These defects were due to reduced activation of EC-specific genes concomitant with lower enrichment of histone 3 acetylation at Lys27 (H3K27) at their promoters. We hypothesized that overexpression of Cited2 in Vezf1−/− cells sequesters P300/CBP away from the promoters of proangiogenic genes and thereby contributes to defective angiogenesis in these cells. This idea was supported by the observation that shRNA-mediated depletion of Cited2 significantly reduces the angiogenic defects in the Vezf1−/− ECs. In contrast to previous studies that have focused on the role of Vezf1 as a transcriptional activator of proangiogenic genes, our findings have revealed a role for Vezf1 in modulating the expression of the antiangiogenic factor Cited2. Vezf1 previously has been characterized as an insulator protein, and our results now provide insights into the mechanism, indicating that Vezf1 can block inappropriate, nonspecific interactions of promoters with cis-located enhancers, preventing aberrant promoter activation.
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Affiliation(s)
| | - Ming He
- From the Department of Biochemistry and
| | | | | | - Humaira Gowher
- From the Department of Biochemistry and .,Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907
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11
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Tanaka T, Izawa K, Maniwa Y, Okamura M, Okada A, Yamaguchi T, Shirakura K, Maekawa N, Matsui H, Ishimoto K, Hino N, Nakagawa O, Aird WC, Mizuguchi H, Kawabata K, Doi T, Okada Y. ETV2-TET1/TET2 Complexes Induce Endothelial Cell-Specific Robo4 Expression via Promoter Demethylation. Sci Rep 2018; 8:5653. [PMID: 29618782 PMCID: PMC5884809 DOI: 10.1038/s41598-018-23937-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 03/23/2018] [Indexed: 01/18/2023] Open
Abstract
Although transcription factors regulating endothelial cell (EC)-specific gene expression have been identified, it is not known how those factors induce EC-specificity. We previously reported that DNA hypomethylation of the proximal promoter elicits EC-specific expression of Roundabout4 (Robo4). However, the mechanisms establishing EC-specific hypomethylation of the Robo4 promoter remain unknown. In this study, we demonstrated that the hypermethylated Robo4 proximal promoter is demethylated as human iPS cells differentiate into endothelial cells. Reporter assays demonstrated that ETV2, an ETS family transcription factor, bound to ETS motifs in the proximal promoter and activated Robo4 expression. Immunoprecipitation demonstrated direct interaction between ETV2 and methylcytosine-converting enzymes TET1 and TET2. Adenoviral expression of ETV2-TET1/TET2 complexes demethylated the Robo4 promoter and induced Robo4 expression in non-ECs. In summary, we propose a novel regulatory model of EC-specific gene expression via promoter demethylation induced by ETV2-TET1/TET2 complexes during endothelial differentiation.
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Affiliation(s)
- Toru Tanaka
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita City, Osaka, 565-0871, Japan
| | - Kohei Izawa
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita City, Osaka, 565-0871, Japan
| | - Yusuke Maniwa
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita City, Osaka, 565-0871, Japan
| | - Maki Okamura
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita City, Osaka, 565-0871, Japan
| | - Atsumasa Okada
- Laboratory of Stem Cell Regulation, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki City, Osaka, 567-0085, Japan
| | - Tomoko Yamaguchi
- Laboratory of Stem Cell Regulation, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki City, Osaka, 567-0085, Japan
| | - Keisuke Shirakura
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita City, Osaka, 565-0871, Japan
| | - Naoki Maekawa
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita City, Osaka, 565-0871, Japan
| | - Hayato Matsui
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita City, Osaka, 565-0871, Japan
| | - Kenji Ishimoto
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita City, Osaka, 565-0871, Japan
| | - Nobumasa Hino
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita City, Osaka, 565-0871, Japan
| | - Osamu Nakagawa
- Department of Molecular Physiology, National Cerebral and Cardiovascular Center Research Institute, Suita City, Osaka, 565-8565, Japan
| | - William C Aird
- Center for Vascular Biology Research and Division of Molecular and Vascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA
| | - Hiroyuki Mizuguchi
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita City, Osaka, 565-0871, Japan
| | - Kenji Kawabata
- Laboratory of Stem Cell Regulation, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki City, Osaka, 567-0085, Japan
| | - Takefumi Doi
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita City, Osaka, 565-0871, Japan
| | - Yoshiaki Okada
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita City, Osaka, 565-0871, Japan.
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12
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MicroRNAs: Important Regulators of Induced Pluripotent Stem Cell Generation and Differentiation. Stem Cell Rev Rep 2017; 14:71-81. [DOI: 10.1007/s12015-017-9785-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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13
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Liang J, Huang W, Cai W, Wang L, Guo L, Paul C, Yu XY, Wang Y. Inhibition of microRNA-495 Enhances Therapeutic Angiogenesis of Human Induced Pluripotent Stem Cells. Stem Cells 2017; 35:337-350. [DOI: 10.1002/stem.2477] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Abstract
Abstract
Therapeutic angiogenesis has emerged as a promising strategy to regenerate the damaged blood vessels resulting from ischemic diseases such as myocardial infarction (MI). However, the functional integration of implanted endothelial cells (ECs) in infarcted heart remains challenging. We herein develop an EC generation approach by inhibiting microRNA-495 (miR-495) in human induced pluripotent stem cells (hiPSCs) and assess the angiogenic potential for MI treatment. The anti-angiogenic miR-495 belonging to Dlk1-Dio3 miR cluster was identified through expression profiling and computational analysis. Loss-of-function experiments for miR-495 were performed using a lentiviral transfer of antisense sequence in hiPSCs. The pluripotency of hiPSCs was not impacted by the genetic modification. Induced with differentiation medium, miR-495 inhibition enhanced the expression of EC genes of hiPSCs, as well as the yield of ECs. Newly derived ECs displayed prominent angiogenic characteristics including tube formation, cell migration, and proliferation. Mechanistically, miR-495 mediated the expression of endothelial or angiogenic genes by directly targeting vascular endothelial zinc finger 1. After transplantation in immunodeficient MI mice, the derived ECs significantly increased neovascularization in the infarcted heart, prevented functional worsening, and attenuated expansion of infarct size. The functional integration of the implanted ECs into coronary networks was also enhanced by inhibiting miR-495. miR-495 represents a new target not only for promoting EC generation from hiPSCs but also for enhancing angiogenesis and engraftment of hiPSC-derived ECs in ischemic heart.
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Affiliation(s)
- Jialiang Liang
- a Departments of Pathology and Laboratory Medicine, College of Medicine, University of Cincinnati Medical Center, Cincinnati, Ohio, USA
| | - Wei Huang
- a Departments of Pathology and Laboratory Medicine, College of Medicine, University of Cincinnati Medical Center, Cincinnati, Ohio, USA
| | - Wenfeng Cai
- a Departments of Pathology and Laboratory Medicine, College of Medicine, University of Cincinnati Medical Center, Cincinnati, Ohio, USA
| | - Lei Wang
- a Departments of Pathology and Laboratory Medicine, College of Medicine, University of Cincinnati Medical Center, Cincinnati, Ohio, USA
| | - Linlin Guo
- a Departments of Pathology and Laboratory Medicine, College of Medicine, University of Cincinnati Medical Center, Cincinnati, Ohio, USA
| | - Christian Paul
- a Departments of Pathology and Laboratory Medicine, College of Medicine, University of Cincinnati Medical Center, Cincinnati, Ohio, USA
| | - Xi-Yong Yu
- b Institute of Molecular and Clinical Pharmacology, School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Yigang Wang
- a Departments of Pathology and Laboratory Medicine, College of Medicine, University of Cincinnati Medical Center, Cincinnati, Ohio, USA
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14
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Burger NB, Bekker MN, de Groot CJM, Christoffels VM, Haak MC. Why increased nuchal translucency is associated with congenital heart disease: a systematic review on genetic mechanisms. Prenat Diagn 2015; 35:517-28. [DOI: 10.1002/pd.4586] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 12/09/2014] [Accepted: 02/21/2015] [Indexed: 12/15/2022]
Affiliation(s)
- Nicole B. Burger
- Department of Obstetrics and Gynaecology; VU University Medical Center; Amsterdam The Netherlands
| | - Mireille N. Bekker
- Department of Obstetrics and Gynaecology; Radboud University Medical Center; Nijmegen The Netherlands
| | | | - Vincent M. Christoffels
- Department of Anatomy, Embryology & Physiology; Academic Medical Center; Amsterdam The Netherlands
| | - Monique C. Haak
- Department of Obstetrics; Leiden University Medical Center; Leiden The Netherlands
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15
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Okada Y. [Regulation of endothelial cell-specific Robo4 gene expression by DNA methylation and non-lineage specific transcription factors]. YAKUGAKU ZASSHI 2014; 134:817-21. [PMID: 24989473 DOI: 10.1248/yakushi.13-00258] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
Studies of tissue-specific gene expression have suggested that tissue-specific transcription factors or tissue-specific combinations of non-cell-type-specific transcription factors regulate tissue-specific gene expression. Although the studies of endothelial cell (EC)-specific gene expression has identified several transcriptional activators such as SP1, ETS family proteins, and GATA proteins, their expression and combinations are not likely to be EC-specific. To investigate the mechanism of EC-specific gene expression, we analyzed the regulation mechanism of an EC-specific gene, Roundabout4 (Robo4). We identified the 3-kb Robo4 promoter and several transcription factors including SP1 and GABP that bind to the Robo4 promoter and promote Robo4 gene expression. However, we could not explain the mechanism for EC-specific Robo4 gene expression with only those factors because their expression and combination are not EC-specific. Therefore, we hypothesized the contribution of other mechanisms, especially epigenetic control, to Robo4 gene regulation and demonstrated the importance of DNA methylation for EC-specific Robo4 expression. In this review, we summarize our recent studies and discuss the novel regulation model of Robo4 gene expression by transcription factors and DNA methylation.
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Affiliation(s)
- Yoshiaki Okada
- Graduate School of Pharmaceutical Sciences, Osaka University
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Bruderer M, Alini M, Stoddart MJ. Role of HOXA9 and VEZF1 in endothelial biology. J Vasc Res 2013; 50:265-78. [PMID: 23921720 DOI: 10.1159/000353287] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 03/15/2013] [Indexed: 11/19/2022] Open
Abstract
Proper development of the vascular system as one of the earliest and most critical steps during vertebrate embryogenesis is ensured by the exact spatial and temporal control of gene expression in cells forming the vessel network. Whereas the regulation of vascular system development is well elucidated on the level of ligand-receptor signaling, the processes on the transcriptional level are much less understood. As the signaling mechanisms in embryogenesis and pathological conditions are similar, the study of embryonic blood vessel development is of great interest for the treatment of cardiovascular diseases and cancer. This review discusses two transcription factors, HOXA9 and VEZF1, which are relevant for endothelial biology but are excluded in the bulk of transcription factor references discussing endothelial biology. To our knowledge, there is no comprehensive overview of these two transcription factors available to date. Here, we summarize the current knowledge of human HOXA9 and VEZF1 biology and function, we detail their target genes and roles in endothelial biology and propose that HOXA9 and VEZF1 also deserve consideration as relevant transcriptional regulators of endothelial biology. Due to their broad role in multiple aspects of endothelial biology, they might potentially become interesting targets for therapeutic manipulation of pathological blood vessel growth.
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Affiliation(s)
- Marco Bruderer
- Musculoskeletal Regeneration Program, AO Research Institute Davos, Davos, Switzerland
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