1
|
He C, Zhu B, Gao W, Wu Q, Zhang C. Study on Allele Specific Expression of Long-Term Residents in High Altitude Areas. Evol Bioinform Online 2024; 20:11769343241257344. [PMID: 38826865 PMCID: PMC11141219 DOI: 10.1177/11769343241257344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 05/07/2024] [Indexed: 06/04/2024] Open
Abstract
In diploid organisms, half of the chromosomes in each cell come from the father and half from the mother. Through previous studies, it was found that the paternal chromosome and the maternal chromosome can be regulated and expressed independently, leading to the emergence of allele specific expression (ASE). In this study, we analyzed the differential expression of alleles in the high-altitude population and the normal population based on the RNA sequencing data. Through gene cluster analysis and protein interaction network analysis, we found some changes occurred at the gene level, and some negative effects. During the study, we realized that the calmodulin homology domain may have a certain correlation with long-term survival at high altitude. The plateau environment is characterized by hypoxia, low air pressure, strong ultraviolet radiation, and low temperature. Accordingly, the genetic changes in the process of adaptation are mainly reflected in these characteristics. High altitude generation living is also highly related to cancer, immune disease, cardiovascular disease, neurological disease, endocrine disease, and other diseases. Therefore, the medical system in high altitude areas should pay more attention to these diseases.
Collapse
Affiliation(s)
- Chao He
- The General Hospital of Tibet Military Region, Lhasa, China
| | - Bin Zhu
- The General Hospital of Tibet Military Region, Lhasa, China
| | - Wenwen Gao
- The General Hospital of Tibet Military Region, Lhasa, China
| | - Qianjin Wu
- The General Hospital of Tibet Military Region, Lhasa, China
| | | |
Collapse
|
2
|
Svensson E, von Mentzer U, Stubelius A. Achieving Precision Healthcare through Nanomedicine and Enhanced Model Systems. ACS MATERIALS AU 2024; 4:162-173. [PMID: 38496040 PMCID: PMC10941278 DOI: 10.1021/acsmaterialsau.3c00073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/17/2023] [Accepted: 11/28/2023] [Indexed: 03/19/2024]
Abstract
The ability to customize medical choices according to an individual's genetic makeup and biomarker patterns marks a significant advancement toward overall improved healthcare for both individuals and society at large. By transitioning from the conventional one-size-fits-all approach to tailored treatments that can account for predispositions of different patient populations, nanomedicines can be customized to target the specific molecular underpinnings of a patient's disease, thus mitigating the risk of collateral damage. However, for these systems to reach their full potential, our understanding of how nano-based therapeutics behave within the intricate human body is necessary. Effective drug administration to the targeted organ or pathological niche is dictated by properties such as nanocarrier (NC) size, shape, and targeting abilities, where understanding how NCs change their properties when they encounter biomolecules and phenomena such as shear stress in flow remains a major challenge. This Review specifically focuses on vessel-on-a-chip technology that can provide increased understanding of NC behavior in blood and summarizes the specialized environment of the joint to showcase advanced tissue models as approaches to address translational challenges. Compared to conventional cell studies or animal models, these advanced models can integrate patient material for full customization. Combining such models with nanomedicine can contribute to making personalized medicine achievable.
Collapse
Affiliation(s)
| | | | - Alexandra Stubelius
- Division of Chemical Biology,
Department of Life Sciences, Chalmers University
of Technology, Gothenburg 412 96, Sweden
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Dubourg V, Schwerdt G, Schreier B, Kopf M, Mildenberger S, Benndorf RA, Gekle M. EGFR activation differentially affects the inflammatory profiles of female human aortic and coronary artery endothelial cells. Sci Rep 2023; 13:22827. [PMID: 38129563 PMCID: PMC10739936 DOI: 10.1038/s41598-023-50148-7] [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: 09/04/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023] Open
Abstract
Endothelial cells (EC) are key players in vascular function, homeostasis and inflammation. EC show substantial heterogeneity due to inter-individual variability (e.g. sex-differences) and intra-individual differences as they originate from different organs or vessels. This variability may lead to different responsiveness to external stimuli. Here we compared the responsiveness of female human primary EC from the aorta (HAoEC) and coronary arteries (HCAEC) to Epidermal Growth Factor Receptor (EGFR) activation. EGFR is an important signal integration hub for vascular active substances with physiological and pathophysiological relevance. Our transcriptomic analysis suggested that EGFR activation differentially affects the inflammatory profiles of HAoEC and HCAEC, particularly by inducing a HCAEC-driven leukocyte attraction but a downregulation of adhesion molecule and chemoattractant expression in HAoEC. Experimental assessments of selected inflammation markers were performed to validate these predictions and the results confirmed a dual role of EGFR in these cells: its activation initiated an anti-inflammatory response in HAoEC but a pro-inflammatory one in HCAEC. Our study highlights that, although they are both arterial EC, female HAoEC and HCAEC are distinguishable with regard to the role of EGFR and its involvement in inflammation regulation, what may be relevant for vascular maintenance but also the pathogenesis of endothelial dysfunction.
Collapse
Affiliation(s)
- Virginie Dubourg
- Julius-Bernstein-Institute of Physiology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 6, 06112, Halle, Germany.
| | - Gerald Schwerdt
- Julius-Bernstein-Institute of Physiology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 6, 06112, Halle, Germany
| | - Barbara Schreier
- Julius-Bernstein-Institute of Physiology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 6, 06112, Halle, Germany
| | - Michael Kopf
- Julius-Bernstein-Institute of Physiology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 6, 06112, Halle, Germany
| | - Sigrid Mildenberger
- Julius-Bernstein-Institute of Physiology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 6, 06112, Halle, Germany
| | - Ralf A Benndorf
- Department of Clinical Pharmacy and Pharmacotherapy, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Michael Gekle
- Julius-Bernstein-Institute of Physiology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 6, 06112, Halle, Germany
| |
Collapse
|
5
|
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: 3] [Impact Index Per Article: 3.0] [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.
Collapse
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
| |
Collapse
|
6
|
Spanjersberg TCF, Oosterhoff LA, Kruitwagen HS, van den Dungen NAM, Vernooij JCM, Asselbergs FW, Mokry M, Spee B, Harakalova M, van Steenbeek FG. Locational memory of macrovessel vascular cells is transcriptionally imprinted. Sci Rep 2023; 13:13028. [PMID: 37563195 PMCID: PMC10415317 DOI: 10.1038/s41598-023-38880-6] [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: 02/17/2023] [Accepted: 07/17/2023] [Indexed: 08/12/2023] Open
Abstract
Vascular pathologies show locational predisposition throughout the body; further insights into the transcriptomics basis of this vascular heterogeneity are needed. We analyzed transcriptomes from cultured endothelial cells and vascular smooth muscle cells from nine adult canine macrovessels: the aorta, coronary artery, vena cava, portal vein, femoral artery, femoral vein, saphenous vein, pulmonary vein, and pulmonary artery. We observed that organ-specific expression patterns persist in vitro, indicating that these genes are not regulated by blood flow or surrounding cell types but are likely fixed in the epigenetic memory. We further demonstrated the preserved location-specific expression of GATA4 protein in cultured cells and in the primary adult vessel. On a functional level, arterial and venous endothelial cells differed in vascular network morphology as the arterial networks maintained a higher complexity. Our findings prompt the rethinking of the extrapolation of results from single-origin endothelial cell systems.
Collapse
Affiliation(s)
- Talitha C F Spanjersberg
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 104, Utrecht, The Netherlands
- Regenerative Medicine Centre Utrecht, University Medical Center Utrecht, Utrecht University, Uppsalalaan 8, Utrecht, The Netherlands
- Division Heart and Lungs, Department of Cardiology, Circulatory Health Research Center, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, Utrecht, The Netherlands
| | - Loes A Oosterhoff
- Regenerative Medicine Centre Utrecht, University Medical Center Utrecht, Utrecht University, Uppsalalaan 8, Utrecht, The Netherlands
| | - Hedwig S Kruitwagen
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 104, Utrecht, The Netherlands
| | - Noortje A M van den Dungen
- Central Diagnostics Laboratory, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Johannes C M Vernooij
- Department of Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, The Netherlands
| | - Folkert W Asselbergs
- Department of Cardiology, Amsterdam University Medical Centers, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
- Health Data Research UK and Institute of Health Informatics, University College London, London, UK
| | - Michal Mokry
- Central Diagnostics Laboratory, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Laboratory of Experimental Cardiology, Department of Cardiology, University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
| | - Bart Spee
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 104, Utrecht, The Netherlands
- Regenerative Medicine Centre Utrecht, University Medical Center Utrecht, Utrecht University, Uppsalalaan 8, Utrecht, The Netherlands
| | - Magdalena Harakalova
- Regenerative Medicine Centre Utrecht, University Medical Center Utrecht, Utrecht University, Uppsalalaan 8, Utrecht, The Netherlands
- Division Heart and Lungs, Department of Cardiology, Circulatory Health Research Center, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, Utrecht, The Netherlands
| | - Frank G van Steenbeek
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 104, Utrecht, The Netherlands.
- Regenerative Medicine Centre Utrecht, University Medical Center Utrecht, Utrecht University, Uppsalalaan 8, Utrecht, The Netherlands.
- Division Heart and Lungs, Department of Cardiology, Circulatory Health Research Center, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, Utrecht, The Netherlands.
| |
Collapse
|
7
|
McNamara ME, Loyfer N, Kiliti AJ, Schmidt MO, Shabi-Porat S, Jain SS, Martinez Roth S, McDeed AP, Shahrour N, Ballew E, Lin YT, Li HH, Deslattes Mays A, Rudra S, Riegel AT, Unger K, Kaplan T, Wellstein A. Circulating cell-free methylated DNA reveals tissue-specific, cellular damage from radiation treatment. JCI Insight 2023; 8:e156529. [PMID: 37318863 PMCID: PMC10443812 DOI: 10.1172/jci.insight.156529] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 05/31/2023] [Indexed: 06/17/2023] Open
Abstract
Radiation therapy is an effective cancer treatment, although damage to healthy tissues is common. Here we analyzed cell-free, methylated DNA released from dying cells into the circulation to evaluate radiation-induced cellular damage in different tissues. To map the circulating DNA fragments to human and mouse tissues, we established sequencing-based, cell-type-specific reference DNA methylation atlases. We found that cell-type-specific DNA blocks were mostly hypomethylated and located within signature genes of cellular identity. Cell-free DNA fragments were captured from serum samples by hybridization to CpG-rich DNA panels and mapped to the DNA methylation atlases. In a mouse model, thoracic radiation-induced tissue damage was reflected by dose-dependent increases in lung endothelial and cardiomyocyte methylated DNA in serum. The analysis of serum samples from patients with breast cancer undergoing radiation treatment revealed distinct dose-dependent and tissue-specific epithelial and endothelial responses to radiation across multiple organs. Strikingly, patients treated for right-sided breast cancers also showed increased hepatocyte and liver endothelial DNA in the circulation, indicating the impact on liver tissues. Thus, changes in cell-free methylated DNA can uncover cell-type-specific effects of radiation and provide a readout of the biologically effective radiation dose received by healthy tissues.
Collapse
Affiliation(s)
- Megan E. McNamara
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | - Netanel Loyfer
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Amber J. Kiliti
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | - Marcel O. Schmidt
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | - Sapir Shabi-Porat
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sidharth S. Jain
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | - Sarah Martinez Roth
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | - A. Patrick McDeed
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | - Nesreen Shahrour
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | | | - Yun-Tien Lin
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | - Heng-Hong Li
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | | | - Sonali Rudra
- Medstar Georgetown University Hospital, Washington DC, USA
| | - Anna T. Riegel
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | - Keith Unger
- Medstar Georgetown University Hospital, Washington DC, USA
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
- Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Anton Wellstein
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| |
Collapse
|
8
|
Naserinejad N, Costanian C, Birot O, Barboni T, Roudier E. Wildland fire, air pollution and cardiovascular health: is it time to focus on the microvasculature as a risk assessment tool? Front Physiol 2023; 14:1225195. [PMID: 37538378 PMCID: PMC10394245 DOI: 10.3389/fphys.2023.1225195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 07/06/2023] [Indexed: 08/05/2023] Open
Abstract
Climate change favors weather conditions conducive to wildland fires. The intensity and frequency of forest fires are increasing, and fire seasons are lengthening. Exposure of human populations to smoke emitted by these fires increases, thereby contributing to airborne pollution through the emission of gas and particulate matter (PM). The adverse health outcomes associated with wildland fire exposure represent an important burden on the economies and health systems of societies. Even though cardiovascular diseases (CVDs) are the main of cause of the global burden of diseases attributable to PM exposure, it remains difficult to show reliable associations between exposure to wildland fire smoke and cardiovascular disease risk in population-based studies. Optimal health requires a resilient and adaptable network of small blood vessels, namely, the microvasculature. Often alterations of this microvasculature precede the occurrence of adverse health outcomes, including CVD. Biomarkers of microvascular health could then represent possible markers for the early detection of poor cardiovascular outcomes. This review aims to synthesize the current literature to gauge whether assessing the microvasculature can better estimate the cardiovascular impact of wildland fires.
Collapse
Affiliation(s)
- Nazgol Naserinejad
- School of Global Health, Faculty of Health, York University, Toronto, ON, Canada
| | - Christy Costanian
- School of Global Health, Faculty of Health, York University, Toronto, ON, Canada
- Department of Family and Community Medicine, St. Michael’s Hospital, Toronto, ON, Canada
| | - Olivier Birot
- Muscle Health Research Center, School of Kinesiology and Health Science, Faculty of Health, York University, Toronto, ON, Canada
| | - Toussaint Barboni
- Laboratoire des Sciences Pour l’Environnement (SPE), UMR-CNRS 6134, University of Corsica Pasquale Paoli, Campus Grimaldi, Corte, France
| | - Emilie Roudier
- School of Global Health, Faculty of Health, York University, Toronto, ON, Canada
- Muscle Health Research Center, School of Kinesiology and Health Science, Faculty of Health, York University, Toronto, ON, Canada
| |
Collapse
|
9
|
Yoo H, La H, Park C, Yoo S, Lee H, Song H, Do JT, Choi Y, Hong K. Common and distinct functions of mouse Dot1l in the regulation of endothelial transcriptome. Front Cell Dev Biol 2023; 11:1176115. [PMID: 37397258 PMCID: PMC10311421 DOI: 10.3389/fcell.2023.1176115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 06/06/2023] [Indexed: 07/04/2023] Open
Abstract
Epigenetic mechanisms are mandatory for endothelial called lymphangioblasts during cardiovascular development. Dot1l-mediated gene transcription in mice is essential for the development and function of lymphatic ECs (LECs). The role of Dot1l in the development and function of blood ECs blood endothelial cells is unclear. RNA-seq datasets from Dot1l-depleted or -overexpressing BECs and LECs were used to comprehensively analyze regulatory networks of gene transcription and pathways. Dot1l depletion in BECs changed the expression of genes involved in cell-to-cell adhesion and immunity-related biological processes. Dot1l overexpression modified the expression of genes involved in different types of cell-to-cell adhesion and angiogenesis-related biological processes. Genes involved in specific tissue development-related biological pathways were altered in Dot1l-depleted BECs and LECs. Dot1l overexpression altered ion transportation-related genes in BECs and immune response regulation-related genes in LECs. Importantly, Dot1l overexpression in BECs led to the expression of genes related to the angiogenesis and increased expression of MAPK signaling pathways related was found in both Dot1l-overexpressing BECs and LECs. Therefore, our integrated analyses of transcriptomics in Dot1l-depleted and Dot1l-overexpressed ECs demonstrate the unique transcriptomic program of ECs and the differential functions of Dot1l in the regulation of gene transcription in BECs and LECs.
Collapse
|
10
|
Parab S, Setten E, Astanina E, Bussolino F, Doronzo G. The tissue-specific transcriptional landscape underlines the involvement of endothelial cells in health and disease. Pharmacol Ther 2023; 246:108418. [PMID: 37088448 DOI: 10.1016/j.pharmthera.2023.108418] [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: 11/05/2022] [Revised: 03/23/2023] [Accepted: 04/17/2023] [Indexed: 04/25/2023]
Abstract
Endothelial cells (ECs) that line vascular and lymphatic vessels are being increasingly recognized as important to organ function in health and disease. ECs participate not only in the trafficking of gases, metabolites, and cells between the bloodstream and tissues but also in the angiocrine-based induction of heterogeneous parenchymal cells, which are unique to their specific tissue functions. The molecular mechanisms regulating EC heterogeneity between and within different tissues are modeled during embryogenesis and become fully established in adults. Any changes in adult tissue homeostasis induced by aging, stress conditions, and various noxae may reshape EC heterogeneity and induce specific transcriptional features that condition a functional phenotype. Heterogeneity is sustained via specific genetic programs organized through the combinatory effects of a discrete number of transcription factors (TFs) that, at the single tissue-level, constitute dynamic networks that are post-transcriptionally and epigenetically regulated. This review is focused on outlining the TF-based networks involved in EC specialization and physiological and pathological stressors thought to modify their architecture.
Collapse
Affiliation(s)
- Sushant Parab
- Department of Oncology, University of Torino, IT, Italy; Candiolo Cancer Institute-IRCCS-FPO, Candiolo, Torino, IT, Italy
| | - Elisa Setten
- Department of Oncology, University of Torino, IT, Italy; Candiolo Cancer Institute-IRCCS-FPO, Candiolo, Torino, IT, Italy
| | - Elena Astanina
- Candiolo Cancer Institute-IRCCS-FPO, Candiolo, Torino, IT, Italy
| | - Federico Bussolino
- Department of Oncology, University of Torino, IT, Italy; Candiolo Cancer Institute-IRCCS-FPO, Candiolo, Torino, IT, Italy.
| | - Gabriella Doronzo
- Department of Oncology, University of Torino, IT, Italy; Candiolo Cancer Institute-IRCCS-FPO, Candiolo, Torino, IT, Italy
| |
Collapse
|
11
|
Davis MJ, Earley S, Li YS, Chien S. Vascular mechanotransduction. Physiol Rev 2023; 103:1247-1421. [PMID: 36603156 PMCID: PMC9942936 DOI: 10.1152/physrev.00053.2021] [Citation(s) in RCA: 50] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 09/26/2022] [Accepted: 10/04/2022] [Indexed: 01/07/2023] Open
Abstract
This review aims to survey the current state of mechanotransduction in vascular smooth muscle cells (VSMCs) and endothelial cells (ECs), including their sensing of mechanical stimuli and transduction of mechanical signals that result in the acute functional modulation and longer-term transcriptomic and epigenetic regulation of blood vessels. The mechanosensors discussed include ion channels, plasma membrane-associated structures and receptors, and junction proteins. The mechanosignaling pathways presented include the cytoskeleton, integrins, extracellular matrix, and intracellular signaling molecules. These are followed by discussions on mechanical regulation of transcriptome and epigenetics, relevance of mechanotransduction to health and disease, and interactions between VSMCs and ECs. Throughout this review, we offer suggestions for specific topics that require further understanding. In the closing section on conclusions and perspectives, we summarize what is known and point out the need to treat the vasculature as a system, including not only VSMCs and ECs but also the extracellular matrix and other types of cells such as resident macrophages and pericytes, so that we can fully understand the physiology and pathophysiology of the blood vessel as a whole, thus enhancing the comprehension, diagnosis, treatment, and prevention of vascular diseases.
Collapse
Affiliation(s)
- Michael J Davis
- Department of Medical Pharmacology and Physiology, University of Missouri, Columbia, Missouri
| | - Scott Earley
- Department of Pharmacology, University of Nevada, Reno, Nevada
| | - Yi-Shuan Li
- Department of Bioengineering, University of California, San Diego, California
- Institute of Engineering in Medicine, University of California, San Diego, California
| | - Shu Chien
- Department of Bioengineering, University of California, San Diego, California
- Institute of Engineering in Medicine, University of California, San Diego, California
- Department of Medicine, University of California, San Diego, California
| |
Collapse
|
12
|
Rincón-Riveros A, De la Peña J, Rubiano W, Olivella F, Martinez-Agüero M, Villegas VE. Primary Breast Angiosarcoma: Comparative Transcriptome Analysis. Int J Mol Sci 2022; 23:ijms232416032. [PMID: 36555675 PMCID: PMC9781631 DOI: 10.3390/ijms232416032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/22/2022] [Accepted: 11/24/2022] [Indexed: 12/23/2022] Open
Abstract
Primary breast angiosarcoma, with de novo appearance and not associated with exposure to radiation or lymphedema, is a rare pathology representing less than 0.05% of the neoplasms related to this organ. The pathology is characterized by its aggressiveness, poor prognosis, and difficulties in its differential diagnosis. This article reports the case of a 55-year-old white woman with no family history of cancer, with a rapidly growing mass in the left mammary gland that ulcerates and bleeds. It is confirmed as primary breast angiosarcoma by immunostaining in the tumor tissue for CD31, CD34, and FLI-1. In addition, a sample of neoplastic and healthy tissues is collected from the patient for RNA sequencing; the results are contrasted with a tissue sample from a patient with Luminal A subtype of breast cancer, as well as data from other cases of angiosarcoma available in public databases. These findings revealed a genetic profile associated with the immune and inflammatory response in the patient's sample when compared to available angiosarcoma data; these molecular patterns are consistent with other recent studies. Due to the rarity of the disease, the studies carried out on each patient contribute to the expanding knowledge of the etiology and molecular pathways that are still partially known and continue to be the subject of research. Aside from a comparative transcriptome study, this article aims to provide an update on the state of knowledge about this disease.
Collapse
Affiliation(s)
- Andrés Rincón-Riveros
- Bioinformatics and Systems Biology Group, Universidad Nacional de Colombia, Bogotá 111221, Colombia
- Correspondence: (A.R.-R.); (V.E.V.); Tel.: +57-1-6012-418800 (ext. 281) (A.R.-R.); +57-1-6012-976200 (ext. 4029) (V.E.V.)
| | - Jairo De la Peña
- Servicio de Mastología, Hospital Universitario Mayor Méderi, Bogotá 111411, Colombia
| | - Wilson Rubiano
- Servicio de Mastología, Hospital Universitario Mayor Méderi, Bogotá 111411, Colombia
| | - Fabio Olivella
- Servicio de Mastología, Hospital Universitario Mayor Méderi, Bogotá 111411, Colombia
| | - María Martinez-Agüero
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia
| | - Victoria E. Villegas
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia
- Correspondence: (A.R.-R.); (V.E.V.); Tel.: +57-1-6012-418800 (ext. 281) (A.R.-R.); +57-1-6012-976200 (ext. 4029) (V.E.V.)
| |
Collapse
|
13
|
Tay KY, Wu KX, Chioh FWJ, Autio MI, Pek NMQ, Narmada BC, Tan SH, Low AFH, Lian MM, Chew EGY, Lau HH, Kao SL, Teo AKK, Foo JN, Foo RSY, Heng CK, Chan MYY, Cheung C. Trans-interaction of risk loci 6p24.1 and 10q11.21 is associated with endothelial damage in coronary artery disease. Atherosclerosis 2022; 362:11-22. [PMID: 36435092 DOI: 10.1016/j.atherosclerosis.2022.10.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 10/18/2022] [Accepted: 10/19/2022] [Indexed: 12/15/2022]
Abstract
BACKGROUND AND AIMS Single nucleotide polymorphism rs6903956 has been identified as one of the genetic risk factors for coronary artery disease (CAD). However, rs6903956 lies in a non-coding locus on chromosome 6p24.1. We aim to interrogate the molecular basis of 6p24.1 containing rs6903956 risk alleles in endothelial disease biology. METHODS AND RESULTS We generated induced pluripotent stem cells (iPSCs) from CAD patients (AA risk genotype at rs6903956) and non-CAD subjects (GG non-risk genotype at rs6903956). CRISPR-Cas9-based deletions (Δ63-89bp) on 6p24.1, including both rs6903956 and a short tandem repeat variant rs140361069 in linkage disequilibrium, were performed to generate isogenic iPSC-derived endothelial cells. Edited CAD endothelial cells, with removal of 'A' risk alleles, exhibited a global transcriptional downregulation of pathways relating to abnormal vascular physiology and activated endothelial processes. A CXC chemokine ligand on chromosome 10q11.21, CXCL12, was uncovered as a potential effector gene in CAD endothelial cells. Underlying this effect was the preferential inter-chromosomal interaction of 6p24.1 risk locus to a weak promoter of CXCL12, confirmed by chromatin conformation capture assays on our iPSC-derived endothelial cells. Functionally, risk genotypes AA/AG at rs6903956 were associated significantly with elevated levels of circulating damaged endothelial cells in CAD patients. Circulating endothelial cells isolated from patients with risk genotypes AA/AG were also found to have 10 folds higher CXCL12 transcript copies/cell than those with non-risk genotype GG. CONCLUSIONS Our study reveals the trans-acting impact of 6p24.1 with another CAD locus on 10q11.21 and is associated with intensified endothelial injury.
Collapse
Affiliation(s)
- Kai Yi Tay
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, 636921, Singapore
| | - Kan Xing Wu
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, 636921, Singapore
| | - Florence Wen Jing Chioh
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, 636921, Singapore
| | - Matias Ilmari Autio
- Genome Institute of Singapore, 60 Biopolis Street, 138672, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - Balakrishnan Chakrapani Narmada
- Genome Institute of Singapore, 60 Biopolis Street, 138672, Singapore; Experimental Drug Development Centre, A*STAR, 10 Biopolis Road, Singapore, 138670
| | - Sock-Hwee Tan
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore; National University Heart Centre, National University Health System, Singapore
| | - Adrian Fatt-Hoe Low
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore; National University Heart Centre, National University Health System, Singapore
| | - Michelle Mulan Lian
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, 636921, Singapore
| | - Elaine Guo Yan Chew
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, 636921, Singapore
| | - Hwee Hui Lau
- Institute of Molecular and Cell Biology (IMCB), A*STAR, Proteos, 138673, Singapore; School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Shih Ling Kao
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Cancer Science Institute of Singapore, National University of Singapore, Singapore; Department of Medicine, National University Hospital and National University Health System, Singapore
| | - Adrian Kee Keong Teo
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Institute of Molecular and Cell Biology (IMCB), A*STAR, Proteos, 138673, Singapore
| | - Jia Nee Foo
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, 636921, Singapore; Genome Institute of Singapore, 60 Biopolis Street, 138672, Singapore
| | - Roger Sik Yin Foo
- Genome Institute of Singapore, 60 Biopolis Street, 138672, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore; National University Heart Centre, National University Health System, Singapore
| | - Chew Kiat Heng
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Khoo Teck Puat, National University Children's Medical Institute, National University Health System, Singapore
| | - Mark Yan Yee Chan
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore; National University Heart Centre, National University Health System, Singapore
| | - Christine Cheung
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, 636921, Singapore; Institute of Molecular and Cell Biology (IMCB), A*STAR, Proteos, 138673, Singapore.
| |
Collapse
|
14
|
Zhang X, Qiu H, Zhang F, Ding S. Advances in Single-Cell Multi-Omics and Application in Cardiovascular Research. Front Cell Dev Biol 2022; 10:883861. [PMID: 35733851 PMCID: PMC9207481 DOI: 10.3389/fcell.2022.883861] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/23/2022] [Indexed: 12/30/2022] Open
Abstract
With the development of ever more powerful and versatile high-throughput sequencing techniques and innovative ways to capture single cells, mapping the multicellular tissues at the single-cell level is becoming routine practice. However, it is still challenging to depict the epigenetic landscape of a single cell, especially the genome-wide chromatin accessibility, histone modifications, and DNA methylation. We summarize the most recent methodologies to profile these epigenetic marks at the single-cell level. We also discuss the development and advancement of several multi-omics sequencing technologies from individual cells. Advantages and limitations of various methods to compare and integrate datasets obtained from different sources are also included with specific practical notes. Understanding the heart tissue at single-cell resolution and multi-modal levels will help to elucidate the cell types and states involved in physiological and pathological events during heart development and disease. The rich information produced from single-cell multi-omics studies will also promote the research of heart regeneration and precision medicine on heart diseases.
Collapse
Affiliation(s)
- Xingwu Zhang
- Center for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing, China
| | - Hui Qiu
- Center for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing, China
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Fengzhi Zhang
- First Hospital of Tsinghua University, Beijing, China
| | - Shuangyuan Ding
- Center for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing, China
| |
Collapse
|
15
|
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.
Collapse
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
| | | |
Collapse
|
16
|
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: 7] [Impact Index Per Article: 3.5] [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.
Collapse
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:
| |
Collapse
|
17
|
Knockdown of Circular Ubiquitin-specific Peptidase 9 X-Linked Alleviates Oxidized Low-density Lipoprotein-induced Injuries of Human Umbilical Vein Endothelial Cells by Mediating the miR-148b-3p/KLF5 Signaling Pathway. J Cardiovasc Pharmacol 2021; 78:809-818. [PMID: 34882112 DOI: 10.1097/fjc.0000000000001127] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 07/15/2021] [Indexed: 12/22/2022]
Abstract
ABSTRACT There is evidence that the development of atherosclerosis (AS) involves the dysregulation of circular RNAs. This study aimed to investigate the role of circular ubiquitin-specific peptidase 9 X-linked (circUSP9X) in AS cell models. Human umbilical vein endothelial cells (HUVECs) treated with oxidized low-density lipoprotein (ox-LDL) were used as cell models of AS. The expression of circUSP9X, miR-148b-3p, and Kruppel-like factor 5 (KLF5) messenger RNA was measured using quantitative polymerase chain reaction. Cell viability was assessed by Cell Counting Kit-8 assay. Lactate dehydrogenase leakage, malonaldehyde content, and superoxide dismutase activity were investigated using matched commercial kits. Cell apoptosis was detected using flow cytometry assay. The protein levels of apoptosis-related markers and KLF5 were detected by western blot. The release of proinflammatory factors was monitored by enzyme-linked immunosorbent assay. The predicted relationship between miR-148b-3p and circUSP9X or KLF5 was confirmed by dual-luciferase reporter assay or RNA immunoprecipitation assay. CircUSP9X was highly expressed in ox-LDL-treated HUVECs. CircUSP9X knockdown inhibited ox-LDL-induced lactate dehydrogenase leakage, apoptosis, inflammation, and oxidative stress in HUVECs. CircUSP9X directly bound to miR-148b-3p, and KLF5 was a target of miR-148b-3p. CircUSP9X could regulate KLF5 expression by competitively targeting miR-148b-3p. Rescue experiments indicated that circUSP9X knockdown inhibited ox-LDL-induced HUVEC injuries by enriching miR-148b-3p, and miR-148b-3p restoration alleviated ox-LDL-induced HUVEC injuries by degrading KLF5. In conclusion, circUSP9X knockdown relieved ox-LDL-triggered HUVEC injuries during AS progression partly by mediating the miR-148b-3p/KLF5 network.
Collapse
|
18
|
Rauti R, Shahoha M, Leichtmann-Bardoogo Y, Nasser R, Paz E, Tamir R, Miller V, Babich T, Shaked K, Ehrlich A, Ioannidis K, Nahmias Y, Sharan R, Ashery U, Maoz BM. Effect of SARS-CoV-2 proteins on vascular permeability. eLife 2021; 10:69314. [PMID: 34694226 PMCID: PMC8545399 DOI: 10.7554/elife.69314] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 10/09/2021] [Indexed: 12/13/2022] Open
Abstract
Severe acute respiratory syndrome (SARS)-CoV-2 infection leads to severe disease associated with cytokine storm, vascular dysfunction, coagulation, and progressive lung damage. It affects several vital organs, seemingly through a pathological effect on endothelial cells. The SARS-CoV-2 genome encodes 29 proteins, whose contribution to the disease manifestations, and especially endothelial complications, is unknown. We cloned and expressed 26 of these proteins in human cells and characterized the endothelial response to overexpression of each, individually. Whereas most proteins induced significant changes in endothelial permeability, nsp2, nsp5_c145a (catalytic dead mutant of nsp5), and nsp7 also reduced CD31, and increased von Willebrand factor expression and IL-6, suggesting endothelial dysfunction. Using propagation-based analysis of a protein–protein interaction (PPI) network, we predicted the endothelial proteins affected by the viral proteins that potentially mediate these effects. We further applied our PPI model to identify the role of each SARS-CoV-2 protein in other tissues affected by coronavirus disease (COVID-19). While validating the PPI network model, we found that the tight junction (TJ) proteins cadherin-5, ZO-1, and β-catenin are affected by nsp2, nsp5_c145a, and nsp7 consistent with the model prediction. Overall, this work identifies the SARS-CoV-2 proteins that might be most detrimental in terms of endothelial dysfunction, thereby shedding light on vascular aspects of COVID-19.
Collapse
Affiliation(s)
- Rossana Rauti
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Meishar Shahoha
- School of Neurobiology, Biochemistry and Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | | | - Rami Nasser
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Eyal Paz
- School of Neurobiology, Biochemistry and Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Rina Tamir
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Victoria Miller
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Tal Babich
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel.,School of Neurobiology, Biochemistry and Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Kfir Shaked
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel.,School of Neurobiology, Biochemistry and Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Avner Ehrlich
- Grass Center for Bioengineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Yaakov Nahmias
- Grass Center for Bioengineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Roded Sharan
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Uri Ashery
- School of Neurobiology, Biochemistry and Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.,The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Ben Meir Maoz
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel.,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.,The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel
| |
Collapse
|
19
|
Vega-Tapia F, Peñaloza E, Krause BJ. Specific arterio-venous transcriptomic and ncRNA-RNA interactions in human umbilical endothelial cells: A meta-analysis. iScience 2021; 24:102675. [PMID: 34222842 PMCID: PMC8243012 DOI: 10.1016/j.isci.2021.102675] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/21/2021] [Accepted: 05/27/2021] [Indexed: 01/06/2023] Open
Abstract
Whether arterial-venous differences of primary endothelial cells commonly used for vascular research are preserved in vitro remains under debate. To address this issue, a meta-analysis of Affymetrix transcriptomic data sets from human umbilical artery (HUAECs) and vein (HUVEC) endothelial cells was performed. The meta-analysis showed 2,742 transcripts differentially expressed (false discovery rate <0.05), of which 78% were downregulated in HUVECs. Comparisons with RNA-seq data sets showed high levels of agreement and correlation (p < 0.0001), identifying 84 arterial-venous identity markers. Functional analysis revealed enrichment of key vascular processes in HUAECs/HUVECs, including nitric oxide- (NO) and hypoxia-related genes, as well as differences in miRNA- and ncRNA-mRNA interaction profiles. A proof of concept of these findings in primary cells exposed to hypoxia in vitro and in vivo confirmed the arterial-venous differences in NO-related genes and miRNAs. Altogether, these data defined a cross-platform arterial-venous transcript profile for cultured HUAEC-HUVEC and support a preserved identity involving key vascular pathways post-transcriptionally regulated in vitro. Transcriptional differences among HUAEC and HUVEC are preserved in culture These differences occur even after correcting for experimental conditions The heterogenous regulation affects NO- and hypoxia-related genes Cell-specific ncRNA/mRNA interactions are found
Collapse
Affiliation(s)
- Fabian Vega-Tapia
- Instituto de Ciencias de la Salud, Universidad de O'Higgins, Avenida Libertador Bernardo O'Higgins 611, Rancagua, Chile
| | - Estefania Peñaloza
- Instituto de Ciencias de la Salud, Universidad de O'Higgins, Avenida Libertador Bernardo O'Higgins 611, Rancagua, Chile
| | - Bernardo J Krause
- Instituto de Ciencias de la Salud, Universidad de O'Higgins, Avenida Libertador Bernardo O'Higgins 611, Rancagua, Chile
| |
Collapse
|
20
|
Lam B, Nwadozi E, Haas TL, Birot O, Roudier E. High Glucose Treatment Limits Drosha Protein Expression and Alters AngiomiR Maturation in Microvascular Primary Endothelial Cells via an Mdm2-dependent Mechanism. Cells 2021; 10:742. [PMID: 33801773 PMCID: PMC8065922 DOI: 10.3390/cells10040742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/20/2021] [Accepted: 03/23/2021] [Indexed: 12/21/2022] Open
Abstract
Diabetes promotes an angiostatic phenotype in the microvascular endothelium of skeletal muscle and skin. Angiogenesis-related microRNAs (angiomiRs) regulate angiogenesis through the translational repression of pro- and anti-angiogenic genes. The maturation of micro-RNA (miRs), including angiomiRs, requires the action of DROSHA and DICER proteins. While hyperglycemia modifies the expression of angiomiRs, it is unknown whether high glucose conditions alter the maturation process of angiomiRs in dermal and skeletal muscle microvascular endothelial cells (MECs). Compared to 5 mM of glucose, high glucose condition (30 mM, 6-24 h) decreased DROSHA protein expression, without changing DROSHA mRNA, DICER mRNA, or DICER protein in primary dermal MECs. Despite DROSHA decreasing, high glucose enhanced the maturation and expression of one angiomiR, miR-15a, and downregulated an miR-15a target: Vascular Endothelial Growth Factor-A (VEGF-A). The high glucose condition increased Murine Double Minute-2 (MDM2) expression and MDM2-binding to DROSHA. Inhibition of MDM2 prevented the effects evoked by high glucose on DROSHA protein and miR-15a maturation in dermal MECs. In db/db mice, blood glucose was negatively correlated with the expression of skeletal muscle DROSHA protein, and high glucose decreased DROSHA protein in skeletal muscle MECs. Altogether, our results suggest that high glucose reduces DROSHA protein and enhances the maturation of the angiostatic miR-15a through a mechanism that requires MDM2 activity.
Collapse
|
21
|
Pereira BMV, Katakia YT, Majumder S, Thieme K. Unraveling the epigenetic landscape of glomerular cells in kidney disease. J Mol Med (Berl) 2021; 99:785-803. [PMID: 33763722 DOI: 10.1007/s00109-021-02066-2] [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: 11/05/2020] [Revised: 03/12/2021] [Accepted: 03/18/2021] [Indexed: 01/19/2023]
Abstract
Chronic kidney disease (CKD) is a major public health concern and its prevalence and incidence are rising quickly. It is a non-communicable disease primarily caused by diabetes and/or hypertension and is associated with high morbidity and mortality. Despite decades of research efforts, the pathogenesis of CKD remains a puzzle with missing pieces. Understanding the cellular and molecular mechanisms that govern the loss of kidney function is crucial. Abrupt regulation of gene expression in kidney cells is apparent in CKD and shown to be responsible for disease onset and progression. Gene expression regulation extends beyond DNA sequence and involves epigenetic mechanisms including changes in DNA methylation and post-translational modifications of histones, driven by the activity of specific enzymes. Recent advances demonstrate the essential participation of epigenetics in kidney (patho)physiology, as its actions regulate both the integrity of cells but also triggers deleterious signaling pathways. Here, we review the known epigenetic processes regulating the complex filtration unit of the kidney, the glomeruli. The review will elaborate on novel insights into how epigenetics contributes to cell injury in the CKD setting majorly focusing on kidney glomerular cells: the glomerular endothelial cells, the mesangial cells, and the specialized and terminally differentiated podocyte cells.
Collapse
Affiliation(s)
- Beatriz Maria Veloso Pereira
- Laboratório de Bases Celulares e Moleculares da Fisiologia Renal, Departamento de Fisiologia e Biofísica, Instituto de Ciências Biomédicas, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Yash T Katakia
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS) Pilani, Pilani Campus, Pilani, Rajasthan, India
| | - Syamantak Majumder
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS) Pilani, Pilani Campus, Pilani, Rajasthan, India
| | - Karina Thieme
- Laboratório de Bases Celulares e Moleculares da Fisiologia Renal, Departamento de Fisiologia e Biofísica, Instituto de Ciências Biomédicas, Universidade de Sao Paulo, Sao Paulo, SP, Brazil.
| |
Collapse
|
22
|
Yoshitomi Y, Ikeda T, Saito-Takatsuji H, Yonekura H. Emerging Role of AP-1 Transcription Factor JunB in Angiogenesis and Vascular Development. Int J Mol Sci 2021; 22:ijms22062804. [PMID: 33802099 PMCID: PMC8000613 DOI: 10.3390/ijms22062804] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/06/2021] [Accepted: 03/09/2021] [Indexed: 02/07/2023] Open
Abstract
Blood vessels are essential for the formation and maintenance of almost all functional tissues. They play fundamental roles in the supply of oxygen and nutrition, as well as development and morphogenesis. Vascular endothelial cells are the main factor in blood vessel formation. Recently, research findings showed heterogeneity in vascular endothelial cells in different tissue/organs. Endothelial cells alter their gene expressions depending on their cell fate or angiogenic states of vascular development in normal and pathological processes. Studies on gene regulation in endothelial cells demonstrated that the activator protein 1 (AP-1) transcription factors are implicated in angiogenesis and vascular development. In particular, it has been revealed that JunB (a member of the AP-1 transcription factor family) is transiently induced in endothelial cells at the angiogenic frontier and controls them on tip cells specification during vascular development. Moreover, JunB plays a role in tissue-specific vascular maturation processes during neurovascular interaction in mouse embryonic skin and retina vasculatures. Thus, JunB appears to be a new angiogenic factor that induces endothelial cell migration and sprouting particularly in neurovascular interaction during vascular development. In this review, we discuss the recently identified role of JunB in endothelial cells and blood vessel formation.
Collapse
|
23
|
Nakato R, Sakata T. Methods for ChIP-seq analysis: A practical workflow and advanced applications. Methods 2021; 187:44-53. [PMID: 32240773 DOI: 10.1016/j.ymeth.2020.03.005] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/17/2020] [Accepted: 03/18/2020] [Indexed: 12/13/2022] Open
Abstract
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a central method in epigenomic research. Genome-wide analysis of histone modifications, such as enhancer analysis and genome-wide chromatin state annotation, enables systematic analysis of how the epigenomic landscape contributes to cell identity, development, lineage specification, and disease. In this review, we first present a typical ChIP-seq analysis workflow, from quality assessment to chromatin-state annotation. We focus on practical, rather than theoretical, approaches for biological studies. Next, we outline various advanced ChIP-seq applications and introduce several state-of-the-art methods, including prediction of gene expression level and chromatin loops from epigenome data and data imputation. Finally, we discuss recently developed single-cell ChIP-seq analysis methodologies that elucidate the cellular diversity within complex tissues and cancers.
Collapse
Affiliation(s)
- Ryuichiro Nakato
- Laboratory of Computational Genomics, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
| | - Toyonori Sakata
- Laboratory of Genome Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
| |
Collapse
|
24
|
Gunawardana H, Romero T, Yao N, Heidt S, Mulder A, Elashoff DA, Valenzuela NM. Tissue-specific endothelial cell heterogeneity contributes to unequal inflammatory responses. Sci Rep 2021; 11:1949. [PMID: 33479269 PMCID: PMC7820348 DOI: 10.1038/s41598-020-80102-w] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/16/2020] [Indexed: 12/30/2022] Open
Abstract
Endothelial cells (EC) coordinate vascular homeostasis and inflammation. In organ transplantation, EC are a direct alloimmune target. We posited that tissue specific heterogeneity of vascular EC may partly underlie the disparate organ-specific alloimmune risk. We examined the vascular endothelial response to inflammation across six primary endothelial beds from four major transplanted organs: the heart, lung, kidney and liver. First, we reanalyzed a public dataset of cardiac allograft rejection and found that endothelial inflammatory response genes were elevated in human cardiac allograft biopsies undergoing rejection compared with stable grafts. Next, the inducible inflammatory phenotypes of EC from heart, lung, kidney, and liver were characterized in vitro, focused on expression of adhesion molecules and chemokines, and recruitment of allogeneic peripheral blood mononuclear immune cells. Large vessel cardiac EC most highly upregulated VCAM-1, particularly compared with hepatic EC, supported greater leukocyte adhesion and had distinct chemokine profiles after stimulation with cytokines and complement. Differentially expressed gene candidates that are known regulators of cytokine signaling and inflammatory programming were verified in publicly available datasets of organ-specific endothelial transcriptomes. In summary, differential baseline expression of immune regulating genes may contribute to differential vascular inflammatory responses depending on organ.
Collapse
Affiliation(s)
- Hasitha Gunawardana
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, 1000 Veteran Avenue, Room 1-520, Los Angeles, CA, 90095, USA
| | - Tahmineh Romero
- Statistics Core, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Ning Yao
- Statistics Core, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Sebastiaan Heidt
- Department of Immunohaematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Arend Mulder
- Department of Immunohaematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - David A Elashoff
- Statistics Core, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Nicole M Valenzuela
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, 1000 Veteran Avenue, Room 1-520, Los Angeles, CA, 90095, USA.
| |
Collapse
|
25
|
Okazaki K, Anzawa H, Liu Z, Ota N, Kitamura H, Onodera Y, Alam MM, Matsumaru D, Suzuki T, Katsuoka F, Tadaka S, Motoike I, Watanabe M, Hayasaka K, Sakurada A, Okada Y, Yamamoto M, Suzuki T, Kinoshita K, Sekine H, Motohashi H. Enhancer remodeling promotes tumor-initiating activity in NRF2-activated non-small cell lung cancers. Nat Commun 2020; 11:5911. [PMID: 33219226 PMCID: PMC7679411 DOI: 10.1038/s41467-020-19593-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 10/21/2020] [Indexed: 01/05/2023] Open
Abstract
Transcriptional dysregulation, which can be caused by genetic and epigenetic alterations, is a fundamental feature of many cancers. A key cytoprotective transcriptional activator, NRF2, is often aberrantly activated in non-small cell lung cancers (NSCLCs) and supports both aggressive tumorigenesis and therapeutic resistance. Herein, we find that persistently activated NRF2 in NSCLCs generates enhancers at gene loci that are not normally regulated by transiently activated NRF2 under physiological conditions. Elevated accumulation of CEBPB in NRF2-activated NSCLCs is found to be one of the prerequisites for establishment of the unique NRF2-dependent enhancers, among which the NOTCH3 enhancer is shown to be critical for promotion of tumor-initiating activity. Enhancer remodeling mediated by NRF2-CEBPB cooperativity promotes tumor-initiating activity and drives malignancy of NRF2-activated NSCLCs via establishment of the NRF2-NOTCH3 regulatory axis. Aberrant activation of NRF2 in cancer cells contributes to tumorigenicity and therapeutic resistance. Here, the authors show that NRF2 cooperates with CEBPB and remodels enhancers to confer tumor-initiating activity on NRF2- activated non-small cell lung cancers.
Collapse
Affiliation(s)
- Keito Okazaki
- Department of Gene Expression Regulation, Institute of Development, Aging and Cancer, Tohoku University, Sendai, 980-8575, Japan
| | - Hayato Anzawa
- Department of System Bioinformatics, Graduate School of Information Sciences, Tohoku University, 980-8579, Sendai, Japan
| | - Zun Liu
- Department of Gene Expression Regulation, Institute of Development, Aging and Cancer, Tohoku University, Sendai, 980-8575, Japan
| | - Nao Ota
- Department of Gene Expression Regulation, Institute of Development, Aging and Cancer, Tohoku University, Sendai, 980-8575, Japan
| | - Hiroshi Kitamura
- Department of Gene Expression Regulation, Institute of Development, Aging and Cancer, Tohoku University, Sendai, 980-8575, Japan
| | - Yoshiaki Onodera
- Department of Anatomic Pathology, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
| | - Md Morshedul Alam
- Department of Gene Expression Regulation, Institute of Development, Aging and Cancer, Tohoku University, Sendai, 980-8575, Japan
| | - Daisuke Matsumaru
- Department of Gene Expression Regulation, Institute of Development, Aging and Cancer, Tohoku University, Sendai, 980-8575, Japan
| | - Takuma Suzuki
- Department of Gene Expression Regulation, Institute of Development, Aging and Cancer, Tohoku University, Sendai, 980-8575, Japan
| | - Fumiki Katsuoka
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8573, Japan
| | - Shu Tadaka
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8573, Japan
| | - Ikuko Motoike
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8573, Japan
| | - Mika Watanabe
- Department of Pathology, Tohoku University Hospital, Sendai, 980-8575, Japan
| | - Kazuki Hayasaka
- Department of Gene Expression Regulation, Institute of Development, Aging and Cancer, Tohoku University, Sendai, 980-8575, Japan.,Department of Thoracic Surgery, Institute of Development, Aging and Cancer, Tohoku University, Sendai, 980-8575, Japan
| | - Akira Sakurada
- Department of Thoracic Surgery, Institute of Development, Aging and Cancer, Tohoku University, Sendai, 980-8575, Japan
| | - Yoshinori Okada
- Department of Thoracic Surgery, Institute of Development, Aging and Cancer, Tohoku University, Sendai, 980-8575, Japan
| | - Masayuki Yamamoto
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8573, Japan.,Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
| | - Takashi Suzuki
- Department of Pathology and Histotechnology, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
| | - Kengo Kinoshita
- Department of System Bioinformatics, Graduate School of Information Sciences, Tohoku University, 980-8579, Sendai, Japan.,Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8573, Japan
| | - Hiroki Sekine
- Department of Gene Expression Regulation, Institute of Development, Aging and Cancer, Tohoku University, Sendai, 980-8575, Japan.
| | - Hozumi Motohashi
- Department of Gene Expression Regulation, Institute of Development, Aging and Cancer, Tohoku University, Sendai, 980-8575, Japan.
| |
Collapse
|
26
|
Xin J, Zhang H, He Y, Duren Z, Bai C, Chen L, Luo X, Yan DS, Zhang C, Zhu X, Yuan Q, Feng Z, Cui C, Qi X, Ouzhuluobu, Wong WH, Wang Y, Su B. Chromatin accessibility landscape and regulatory network of high-altitude hypoxia adaptation. Nat Commun 2020; 11:4928. [PMID: 33004791 PMCID: PMC7529806 DOI: 10.1038/s41467-020-18638-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 09/03/2020] [Indexed: 12/27/2022] Open
Abstract
High-altitude adaptation of Tibetans represents a remarkable case of natural selection during recent human evolution. Previous genome-wide scans found many non-coding variants under selection, suggesting a pressing need to understand the functional role of non-coding regulatory elements (REs). Here, we generate time courses of paired ATAC-seq and RNA-seq data on cultured HUVECs under hypoxic and normoxic conditions. We further develop a variant interpretation methodology (vPECA) to identify active selected REs (ASREs) and associated regulatory network. We discover three causal SNPs of EPAS1, the key adaptive gene for Tibetans. These SNPs decrease the accessibility of ASREs with weakened binding strength of relevant TFs, and cooperatively down-regulate EPAS1 expression. We further construct the downstream network of EPAS1, elucidating its roles in hypoxic response and angiogenesis. Collectively, we provide a systematic approach to interpret phenotype-associated noncoding variants in proper cell types and relevant dynamic conditions, to model their impact on gene regulation.
Collapse
Affiliation(s)
- Jingxue Xin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China
- CEMS, NCMIS, MDIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, 100190, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223, Kunming, China
- Bio-X Program, Stanford University, Stanford, CA, 94305, USA
- University of Chinese Academy of Sciences, 100101, Beijing, China
| | - Hui Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223, Kunming, China
| | - Yaoxi He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223, Kunming, China
- University of Chinese Academy of Sciences, 100101, Beijing, China
| | - Zhana Duren
- Departments of Statistics, Stanford University, Stanford, CA, 94305, USA
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, Greenwood, SC, 29646, USA
| | - Caijuan Bai
- High Altitude Medical Research Center, School of Medicine, Tibetan University, 850000, Lhasa, China
| | - Lang Chen
- CEMS, NCMIS, MDIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, 100190, Beijing, China
- University of Chinese Academy of Sciences, 100101, Beijing, China
| | - Xin Luo
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223, Kunming, China
- University of Chinese Academy of Sciences, 100101, Beijing, China
| | - Dong-Sheng Yan
- School of Mathematical Science, Inner Mongolia University, 010021, Huhhot, China
| | - Chaoyu Zhang
- CEMS, NCMIS, MDIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, 100190, Beijing, China
- University of Chinese Academy of Sciences, 100101, Beijing, China
| | - Xiang Zhu
- Departments of Statistics, Stanford University, Stanford, CA, 94305, USA
| | - Qiuyue Yuan
- CEMS, NCMIS, MDIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, 100190, Beijing, China
- University of Chinese Academy of Sciences, 100101, Beijing, China
| | - Zhanying Feng
- CEMS, NCMIS, MDIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, 100190, Beijing, China
- University of Chinese Academy of Sciences, 100101, Beijing, China
| | - Chaoying Cui
- High Altitude Medical Research Center, School of Medicine, Tibetan University, 850000, Lhasa, China
| | - Xuebin Qi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223, Kunming, China
| | - Ouzhuluobu
- High Altitude Medical Research Center, School of Medicine, Tibetan University, 850000, Lhasa, China
| | - Wing Hung Wong
- Bio-X Program, Stanford University, Stanford, CA, 94305, USA.
- Departments of Statistics, Stanford University, Stanford, CA, 94305, USA.
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - Yong Wang
- CEMS, NCMIS, MDIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, 100190, Beijing, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223, Kunming, China.
- University of Chinese Academy of Sciences, 100101, Beijing, China.
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 330106, Hangzhou, China.
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223, Kunming, China.
| |
Collapse
|
27
|
Russell-Hallinan A, Watson CJ, O'Dwyer D, Grieve DJ, O'Neill KM. Epigenetic Regulation of Endothelial Cell Function by Nucleic Acid Methylation in Cardiac Homeostasis and Disease. Cardiovasc Drugs Ther 2020; 35:1025-1044. [PMID: 32748033 PMCID: PMC8452583 DOI: 10.1007/s10557-020-07019-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Pathological remodelling of the myocardium, including inflammation, fibrosis and hypertrophy, in response to acute or chronic injury is central in the development and progression of heart failure (HF). While both resident and infiltrating cardiac cells are implicated in these pathophysiological processes, recent evidence has suggested that endothelial cells (ECs) may be the principal cell type responsible for orchestrating pathological changes in the failing heart. Epigenetic modification of nucleic acids, including DNA, and more recently RNA, by methylation is essential for physiological development due to their critical regulation of cellular gene expression. As accumulating evidence has highlighted altered patterns of DNA and RNA methylation in HF at both the global and individual gene levels, much effort has been directed towards defining the precise role of such cell-specific epigenetic changes in the context of HF. Considering the increasingly apparent crucial role that ECs play in cardiac homeostasis and disease, this article will specifically focus on nucleic acid methylation (both DNA and RNA) in the failing heart, emphasising the key influence of these epigenetic mechanisms in governing EC function. This review summarises current understanding of DNA and RNA methylation alterations in HF, along with their specific role in regulating EC function in response to stress (e.g. hyperglycaemia, hypoxia). Improved appreciation of this important research area will aid in further implicating dysfunctional ECs in HF pathogenesis, whilst informing development of EC-targeted strategies and advancing potential translation of epigenetic-based therapies for specific targeting of pathological cardiac remodelling in HF.
Collapse
Affiliation(s)
- Adam Russell-Hallinan
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Chris J Watson
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Denis O'Dwyer
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - David J Grieve
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Karla M O'Neill
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK.
| |
Collapse
|